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- PDB-4hea: Crystal structure of the entire respiratory complex I from Thermu... -

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Basic information

Entry
Database: PDB / ID: 4hea
TitleCrystal structure of the entire respiratory complex I from Thermus thermophilus
Components
  • (NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 15
  • Putative uncharacterized protein TTHA1528
KeywordsOXIDOREDUCTASE / NADH-quinone oxidoreductase / complex I / proton pump / membrane protein / NADH / menaquinone / cytoplasmic membrane
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / respiratory chain complex I / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / iron-sulfur cluster assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / respiratory chain complex I / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / iron-sulfur cluster assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / plasma membrane
Similarity search - Function
NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2700 / TTHA1528-like / NADH-quinone oxidoreductase subunit E / Alpha-Beta Plaits - #3270 / NADH-quinone oxidoreductase, subunit 15 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / hypothetical protein tt1805 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Domain of unknown function DUF3197 ...NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2700 / TTHA1528-like / NADH-quinone oxidoreductase subunit E / Alpha-Beta Plaits - #3270 / NADH-quinone oxidoreductase, subunit 15 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / hypothetical protein tt1805 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Domain of unknown function DUF3197 / TTHA1528-like superfamily / Protein of unknown function (DUF3197) / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / Helix Hairpins - #3510 / Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily / de novo design (two linked rop proteins) / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain / SLBB domain / 2Fe-2S iron-sulfur cluster binding domain / Cro/C1-type helix-turn-helix domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NuoE domain / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Aspartate decarboxylase-like domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Molybdopterin oxidoreductase, 4Fe-4S domain
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 7 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 7 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 10 / NADH-quinone oxidoreductase subunit 11 / NADH-quinone oxidoreductase subunit 12 / NADH-quinone oxidoreductase subunit 13 / NADH-quinone oxidoreductase subunit 14 / Uncharacterized protein / NADH-quinone oxidoreductase subunit 15 / NADH-quinone oxidoreductase subunit 8
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3027 Å
AuthorsBaradaran, R. / Berrisford, J.M. / Minhas, G.S. / Sazanov, L.A.
CitationJournal: Nature / Year: 2013
Title: Crystal structure of the entire respiratory complex I.
Authors: Baradaran, R. / Berrisford, J.M. / Minhas, G.S. / Sazanov, L.A.
History
DepositionOct 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit 5
6: NADH-quinone oxidoreductase subunit 6
9: NADH-quinone oxidoreductase subunit 9
7: NADH-quinone oxidoreductase subunit 15
W: Putative uncharacterized protein TTHA1528
A: NADH-quinone oxidoreductase subunit 7
J: NADH-quinone oxidoreductase subunit 10
K: NADH-quinone oxidoreductase subunit 11
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
H: NADH-quinone oxidoreductase subunit 8
B: NADH-quinone oxidoreductase subunit 1
C: NADH-quinone oxidoreductase subunit 2
D: NADH-quinone oxidoreductase subunit 3
E: NADH-quinone oxidoreductase subunit 4
F: NADH-quinone oxidoreductase subunit 5
G: NADH-quinone oxidoreductase subunit 6
O: NADH-quinone oxidoreductase subunit 9
I: NADH-quinone oxidoreductase subunit 15
X: Putative uncharacterized protein TTHA1528
P: NADH-quinone oxidoreductase subunit 7
R: NADH-quinone oxidoreductase subunit 10
S: NADH-quinone oxidoreductase subunit 11
T: NADH-quinone oxidoreductase subunit 12
U: NADH-quinone oxidoreductase subunit 13
V: NADH-quinone oxidoreductase subunit 14
Q: NADH-quinone oxidoreductase subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,080,57752
Polymers1,074,03832
Non-polymers6,53920
Water0
1
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit 5
6: NADH-quinone oxidoreductase subunit 6
9: NADH-quinone oxidoreductase subunit 9
7: NADH-quinone oxidoreductase subunit 15
W: Putative uncharacterized protein TTHA1528
A: NADH-quinone oxidoreductase subunit 7
J: NADH-quinone oxidoreductase subunit 10
K: NADH-quinone oxidoreductase subunit 11
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
H: NADH-quinone oxidoreductase subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,28926
Polymers537,01916
Non-polymers3,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area87470 Å2
ΔGint-786 kcal/mol
Surface area147530 Å2
MethodPISA
2
B: NADH-quinone oxidoreductase subunit 1
C: NADH-quinone oxidoreductase subunit 2
D: NADH-quinone oxidoreductase subunit 3
E: NADH-quinone oxidoreductase subunit 4
F: NADH-quinone oxidoreductase subunit 5
G: NADH-quinone oxidoreductase subunit 6
O: NADH-quinone oxidoreductase subunit 9
I: NADH-quinone oxidoreductase subunit 15
X: Putative uncharacterized protein TTHA1528
P: NADH-quinone oxidoreductase subunit 7
R: NADH-quinone oxidoreductase subunit 10
S: NADH-quinone oxidoreductase subunit 11
T: NADH-quinone oxidoreductase subunit 12
U: NADH-quinone oxidoreductase subunit 13
V: NADH-quinone oxidoreductase subunit 14
Q: NADH-quinone oxidoreductase subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,28926
Polymers537,01916
Non-polymers3,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area87620 Å2
ΔGint-786 kcal/mol
Surface area147290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.280, 340.890, 263.300
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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NADH-quinone oxidoreductase subunit ... , 15 types, 30 molecules 1B2C3D4E5F6G9O7IAPJRKSLTMUNVHQ

#1: Protein NADH-quinone oxidoreductase subunit 1 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 1 / NDH-1 subunit 1


Mass: 48693.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56222, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH-quinone oxidoreductase subunit 2 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 2 / NDH-1 subunit 2


Mass: 20309.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56221, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-quinone oxidoreductase subunit 3 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 3 / NDH-1 subunit 3


Mass: 86656.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56223, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH-quinone oxidoreductase subunit 4 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 4 / NDH-1 subunit 4


Mass: 46428.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56220, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH-quinone oxidoreductase subunit 5 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 5 / NDH-1 subunit 5


Mass: 23893.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56219, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH-quinone oxidoreductase subunit 6 / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit 6 / NDH-1 subunit 6


Mass: 20262.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56218, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH-quinone oxidoreductase subunit 9 / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit 9 / NDH-1 subunit 9


Mass: 20106.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56224, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-quinone oxidoreductase subunit 15 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 15 / NDH-1 subunit 15


Mass: 14812.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q5SKZ7, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-quinone oxidoreductase subunit 7 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 7 / NDH-1 subunit 7


Mass: 13154.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56217, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-quinone oxidoreductase subunit 10 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 10 / NDH-1 subunit 10


Mass: 18563.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56225, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-quinone oxidoreductase subunit 11 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 11 / NDH-1 subunit 11


Mass: 10002.788 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56226, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-quinone oxidoreductase subunit 12 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 12 / NDH-1 subunit 12


Mass: 65189.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56227, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NADH-quinone oxidoreductase subunit 13 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 13 / NDH-1 subunit 13


Mass: 49247.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56228, NADH:ubiquinone reductase (H+-translocating)
#15: Protein NADH-quinone oxidoreductase subunit 14 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 14 / NDH-1 subunit 14


Mass: 44463.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56229, NADH:ubiquinone reductase (H+-translocating)
#16: Protein NADH-quinone oxidoreductase subunit 8 / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit 8 / NDH-1 subunit 8


Mass: 41034.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q60019, NADH:ubiquinone reductase (H+-translocating)

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Protein , 1 types, 2 molecules WX

#9: Protein Putative uncharacterized protein TTHA1528


Mass: 14201.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cytoplasmic membrane / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SI52

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Non-polymers , 3 types, 20 molecules

#17: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Fe4S4
#18: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#19: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.9568.9
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, sitting drop6100 mM Bis-Tris pH 6.0, 19% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 2.2 mM FOS-CHOLINE-8 fluorinated , VAPOR DIFFUSION, SITTING DROP, temperature 295K
2952vapor diffusion, sitting drop6100 mM Bis-Tris pH 6.0, 24% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 50 mM NDSB-201, VAPOR DIFFUSION, SITTING DROP, temperature 295K
2953vapor diffusion, sitting drop6100 mM Bis-Tris pH 6.0, 26% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.6% DDM, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.9
SYNCHROTRONESRF ID2920.9
SYNCHROTRONESRF ID2930.9
Detector
TypeIDDetectorDateDetails
PSI PILATUS 6M1PIXELSep 23, 2011mirrors
PSI PILATUS 6M2PIXELDec 3, 2011mirrors
PSI PILATUS 6M3PIXELFeb 16, 2011mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(311)SINGLE WAVELENGTHMx-ray1
2Si(311)SINGLE WAVELENGTHMx-ray1
3Si(311)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twinOperator: -h,-k,h+l / Fraction: 0.47
ReflectionResolution: 3.3→40 Å / Num. all: 247920 / Num. obs: 247920 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 99 Å2 / Rmerge(I) obs: 0.251 / Rsym value: 0.251 / Net I/σ(I): 5.1
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.869 / Mean I/σ(I) obs: 1 / Rsym value: 1.869 / % possible all: 99

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
PHENIX(phenix.refine: dev_1041)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3I9V and 4HE8

3i9v

4he8


Resolution: 3.3027→39.998 Å / Isotropic thermal model: TLS and isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.24 / Stereochemistry target values: TWIN_LSQ_F
Details: The data set was anisotropically scaled and truncated to 3.3, 3.5 and 3.3 A resolution along the a*, b* and c* axes, respectively, using the Diffraction Anisotropy Server (http://services. ...Details: The data set was anisotropically scaled and truncated to 3.3, 3.5 and 3.3 A resolution along the a*, b* and c* axes, respectively, using the Diffraction Anisotropy Server (http://services.mbi.ucla.edu/anisoscale/)
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 2427 1.04 %Random, using lattice symmetry information (PHENIX).
Rwork0.2024 ---
obs0.2034 233383 93.66 %-
all-233383 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.4 Å2
Refinement stepCycle: LAST / Resolution: 3.3027→39.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms73808 0 190 0 73998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00876098
X-RAY DIFFRACTIONf_angle_d1.467103780
X-RAY DIFFRACTIONf_dihedral_angle_d18.0327292
X-RAY DIFFRACTIONf_chiral_restr0.11111628
X-RAY DIFFRACTIONf_plane_restr0.00713082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3027-3.370.3081670.28425388X-RAY DIFFRACTION37
3.37-3.44320.3046970.265310229X-RAY DIFFRACTION70
3.4432-3.52320.30421390.248513541X-RAY DIFFRACTION94
3.5232-3.61120.26921570.240214324X-RAY DIFFRACTION98
3.6112-3.70880.30291430.233814430X-RAY DIFFRACTION98
3.7088-3.81780.25641580.22314297X-RAY DIFFRACTION99
3.8178-3.94080.2571430.222114299X-RAY DIFFRACTION98
3.9408-4.08140.26491480.209614375X-RAY DIFFRACTION98
4.0814-4.24460.22231440.205614397X-RAY DIFFRACTION98
4.2446-4.43730.2221570.192914365X-RAY DIFFRACTION98
4.4373-4.67070.24611530.18814381X-RAY DIFFRACTION98
4.6707-4.96250.22971610.184414426X-RAY DIFFRACTION99
4.9625-5.34430.22271630.189814429X-RAY DIFFRACTION99
5.3443-5.87960.23551510.196614372X-RAY DIFFRACTION99
5.8796-6.72470.1991520.194114496X-RAY DIFFRACTION99
6.7247-8.45070.21791200.168914515X-RAY DIFFRACTION99
8.4507-33.92260.21421640.191514580X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-00.00030.00280.00020.00220.00540.07980.00140.04320.00950.03020.0236-0.0288-0.0165-0.00010.6947-0.0033-0.04840.75-0.14290.5104-6.0004-19.1729149.3342
2-0.0002-0.0001-0.00010.0002-0.00030.00030.0127-0.00130.00720.01140.00690.01370.0119-0.013500.79310.06110.03490.721-0.08760.6785-22.8436-28.0809140.1855
30.00120-0.00360.00040.00130.003-0.01490.0022-0.02280.0046-0.00040.0102-0.0104-0.023600.6519-0.01320.15160.6394-0.13810.5075-17.6872-25.0264126.8105
40.01150.00860.00250.01460.00590.0032-0.03030.0349-0.0010.0333-0.0184-0.0141-0.02490.0615-0.03180.4099-0.20480.01690.4522-0.14180.1623-2.6159-30.8533136.0416
50.00160.00820.00270.00110.0030.00450.0007-0.0267-0.01-0.0099-0.0018-0.01990.0113-0.0276-0.02180.1694-0.1394-0.0304-0.0305-0.01740.0091-8.2209-32.679127.4654
6-0.00890.0022-0.01190.01160.00040.00730.0029-0.10370.00290.0452-0.03460.0419-0.0345-0.0273-0.01620.2029-0.18520.12180.0568-0.18030.13821.2519-8.161129.7223
70.01040.00790.00530.0040.00520.00130.0404-0.03370.02080.00080.0243-0.0233-0.02320.01380.03950.2349-0.11410.0896-0.0273-0.16830.114910.8446-5.3129112.6883
80.0002-0.00070.00070.0005-0.0007-0.00020.00950.00060.00180.0128-0.0095-0.0097-0.0104-0.0008-00.2241-0.088-0.0070.15690.04310.15894.2041-49.81127.8901
9-0.00060.00020.00140.0017-0.00420.0110.01520.0040.00360.00930.0193-0.0099-0.0179-0.01440.00390.2331-0.05010.02020.01240.01290.15118.7894-42.6043125.1182
100.0001-0.0004-0.00030.00530.00270.00320.02020.0056-0.01270.00590.00680.00770.0066-0.00050.01740.13040.0382-0.05720.06010.04320.089211.8868-44.8455116.4811
110.00040.00040.0004-0.00030.00050.00050.00520.00070.002-0.00020.0083-0.0062-0.0055-0.0112-00.5226-0.0768-0.1320.5698-0.00140.531517.3831-34.6232121.8903
120.00440.0002-0.00100.00060.0036-0.00060.0036-0.0006-0.0005-0.01370.0015-0.0065-0.0066-0.01130.1669-0.0726-0.05140.1055-0.01630.108618.6162-19.1779128.8106
130.00030.00050.00050.00020.00040.00030.00560.00580.0045-0.0038-0.00160.0048-0.0008-0.006-00.4633-0.1356-0.04140.4835-0.06390.451127.9524-17.1104127.2267
140.0002-0.00010.00020.00030.00010.00010.0001-0.00020.0043-0.00460.0035-0.0004-0.00150.0018-00.7079-0.075-0.03460.7136-0.02940.659131.6217-29.4516123.9912
150.00070.00070.00050.00070.0010.0006-0.0024-0.00770.0033-0.0006-0.00280.00340.004-0.016100.2948-0.0796-0.04850.3515-0.03520.270416.8462-21.3571129.7055
160.00040.00020.000500.00030.00010.0071-0.009-0.0066-0.00180.0084-0.00350.01550.002-00.4967-0.0458-0.05590.5742-0.11120.496717.6996-25.3968135.4489
170.00020.00020.00110.00030.00010.00030.009-0.00460.01220.00470.00020.0029-0.00050.004800.5349-0.1084-0.1670.6195-0.07380.473228.4124-21.8541138.3435
180.0003-0.00010.00030.00060.00030.0004-0.00220.00050.0002-0.0026-0.0015-0.00220.001-0.0002-01.0643-0.0213-0.05451.1069-0.00671.054525.4297-33.1993142.9311
190.0003-0.00070.00080.00030.00150.0020.0167-0.00170.00680.01120.00750.0056-0.00030.00900.9395-0.0288-0.10640.9969-0.06070.842216.4009-17.199145.1767
200.12930.0493-0.00480.0242-0.00290.0305-0.0493-0.09980.018-0.0059-0.0145-0.0091-0.0906-0.0987-0.0495-0.01530.06240.0838-0.3608-0.11880.2276-7.9615-20.845495.165
210.0780.01090.01990.04220.03980.03260.04650.0233-0.0348-0.01950.0344-0.0165-0.05910.01370.1735-0.0154-0.0601-0.114-0.20410.07670.142410.1774-24.152996.1691
220.02230.0165-0.03920.0202-0.04550.04510.0146-0.14050.06430.06590.01040.0358-0.05520.0518-0.0018-0.0955-0.22140.0051-0.57940.02570.17835.9481-42.520587.4233
230.00360.00470.00280.01480.0080.0068-0.0227-0.00730.0222-0.0163-0.03390.02440.0277-0.0055-0.0480.0134-0.02550.1789-0.0119-0.01760.23886.5575-70.588860.2178
24-0.0270.0227-0.01480.0115-0.01080.0112-0.0227-0.0167-0.06520.04630.07760.0059-0.0554-0.08060.0982-0.11850.05370.0221-0.589800.0291-11.4171-54.310991.0828
25-0.01790.0117-0.0274-0.0029-0.0069-0.0191-0.03050.0169-0.05860.02820.026-0.07760.00910.07220.0876-0.2651-0.08920.2539-0.54310.26150.3363-8.7839-69.189888.0718
260.0128-0.0088-0.00340.01690.00370.0019-0.02980.053-0.0107-0.0554-0.0535-0.0565-0.05220.0041-0.1182-0.0502-0.0452-0.0579-0.34720.10430.2641-3.0299-57.666766.048
270.0047-0.00220.00750.0241-0.00220.0085-0.0115-0.01540.0065-0.0066-0.07-0.0120.00830.021-0.1269-0.12470.03230.0445-0.07180.02180.2166-1.9149-63.618986.0669
28-0.0003-0.0007-0.00120.00260.00440.00940.0166-0.0001-0.01540.00380.0158-0.0306-0.00180.01020.0310.0402-0.1021-0.0103-0.0070.18210.329610.2086-71.663796.3902
290.0184-0.040.00330.1254-0.01840.04650.05440.15030.0834-0.1140.0191-0.0396-0.0801-0.01780.0858-0.07980.2657-0.0167-0.36980.13180.27425.5223-7.80850.7525
300.00380.00470.00480.00880.00510.01010.0110.0270.05540.0071-0.0103-0.010.01020.0079-0.00580.4055-0.26250.05240.00940.08380.404121.06081.730954.4616
31-0.0001-0.0022-0.00050.0053-0.00570.0038-0.00450.00080.0124-0.0133-0.0074-0.0244-0.0211-0.011-0.00220.46110.31430.05410.36040.23140.4279-0.03237.714338.1684
32-0.0548-0.00120.01740.0154-0.00960.01090.08030.33660.1706-0.0281-0.021-0.0294-0.1704-0.08380.01650.13510.22370.072-0.44920.20140.08714.5724-1.870958.8738
330.0010.0005-0.00070.0011-0.00080.00030.00560.00790.0032-0.00480.003-0.0051-0.00780.0101-01.2450.11720.00961.2799-0.0061.2801-24.33186.534262.2705
34-0-0.0006-0.00010.00070.00190.00060.00020.0041-0.00210.0012-0.00080.0077-0.00860.008600.55850.14590.0680.4281-0.06860.5581-19.1259-3.793366.0023
350.000300.00010.0005-0.00040.00020.0052-0.00860.00290.0059-0.00710.00240.0070.0075-00.51690.1216-0.03880.50070.05190.5496-26.406-3.086652.2138
360.01650.001-0.00750.0062-0.00920.0125-0.00390.02050.0048-0.00370.0332-0.0058-0.0261-0.0090.01010.18840.21050.05310.1030.03260.2928-15.1898-11.1660.2833
370.02340.00230.02510.00040.00390.0345-0.05020.01210.0016-0.0038-0.03480.01050.0063-0.0334-0.00130.30510.14840.23270.24350.06740.4096-13.97082.760953.5933
380.0052-0.0011-0.00140.00370.00050.00490.04990.0173-0.0165-0.01140.03220.00020.00750.00910.00250.35090.25810.10920.24980.06510.4539-19.9084-10.516153.4172
390.0068-0.01-0.00320.0230.0040.00150.01080.0002-0.0062-0.00690.0118-0.0127-0.0130.01040.0080.0553-0.04290.06030.1248-0.05580.1789-11.3747-13.154946.1837
400.0015-0.00630.00040.02280.0003-0.0024-0.00540.00110.0019-0.0028-0.0034-0.0078-0.0029-0.0205-0.0155-0.0311-0.021-0.0303-0.02630.02360.0619-12.1251-18.417844.1475
410.00030.0003-0.00450.01410.00630.00460.03170.0171-0.00520.01250.0354-0.03240.0081-0.01340.083-0.0453-0.0019-0.0591-0.1798-0.10920.14824.1973-30.324361.7645
420.00050.00060.00080.00070.00040.00160.00040.00170.00340.0013-0.00680.0024-0.00120.002900.31610.0033-0.02190.34960.03340.3998-4.138-26.948180.6628
430.0043-0.0005-0.00240.00060.00010.002-0.0045-0.0027-0.00730.0036-0.0047-0.00060.00050.0016-0.00670.08310.0452-0.01220.00090.03910.0992-3.9269-11.95481.2711
440.0021-0.00240.00040.00590.00020.0001-0.0013-0.00080.0125-0.00020.00160.0030.00070.00140.0071-0.0083-0.02370.0089-0.02910.00020.126539.3228-30.22430.5116
450.00660.00120.00250.0008-0.00040.0008-0.00390.00710.0103-0.019-0.0197-0.02120.01030.0209-0.02540.1353-0.0084-0.01120.03620.12030.12620.9821-14.425441.5975
460.00050.0018-0.00090.0029-0.00140.0008-0.01260.00340.01380.0185-0.0056-0.016-0.0269-0.0025-0.00010.628-0.0514-0.01210.69930.01750.674625.0166-16.612833.0921
470.00720.0024-0.00890.0058-0.0111-0.0003-0.06310.00210.01210.0301-0.049-0.0672-0.029-0.0161-0.0857-0.08640.2682-0.0636-0.40110.00090.311320.5764-26.972544.1357
480.00080.0008-0.00020.0015-0.00260.0006-0.0035-0.00250.0077-0.016-0.0171-0.0032-0.0179-0.01500.4554-0.11450.05430.33760.19550.410225.445712.74731.8846
490.00390.00350.00460.00470.00610.0064-0.01370.00250.01430.0231-0.014-0.0018-0.00560.0035-0.00980.10980.0370.0997-0.00950.04160.175333.7726-6.357752.425
500.00730.00590.00210.00610.00180.0004-0.00410.0044-0.0023-0.0060.0060.00020.0012-0.00090.00460.0828-0.0813-0.0999-0.04050.04070.147730.3924-21.404272.7112
510.00210.00150.00770.0163-0.00230.00090.0001-0.01250.0192-0.0045-0.01120.0092-0.01510.024-0.02190.0157-0.03450.0326-0.10530.02660.189219.3151-26.893573.6138
520.01780.0141-0.010.01950.00290.01480.0158-0.01450.05330.03510.0458-0.0220.00070.02610.08680.0387-0.085-0.0404-0.19750.03850.196723.0262-26.54873.9294
530.00670.00990.00090.05850.02260.01050.02230.0015-0.0375-0.0075-0.02880.0028-0.00110.0012-0.00950.0218-0.0333-0.0884-0.06850.05820.188627.4753-25.438759.2244
540.00620.00370.00480.00290.00150.0068-0.0232-0.0016-0.0135-0.0060.0017-0.0209-0.01560.0142-0.02050.0006-0.0659-0.005-0.1372-0.00320.152637.5402-21.944159.5957
550.0010.0016-0.00080.0002-0.00080.0006-0.00760.00440.00950.0026-0.0074-0.0161-0.0091-0.0082-00.2441-0.095-0.03720.2827-0.04640.23136.6208-11.871169.1819
560.0044-0.0007-0.00460.00010.0010.00590.01380.01570.01980.00280.0137-0.01160.00690.03810.00720.1418-0.0772-0.14270.4431-0.04490.264136.8751-24.4148102.5412
570.03090.00170.01780.00140.0040.0240.0291-0.0360.00730.00050.0184-0.01490.00630.00670.0589-0.0329-0.0968-0.0588-0.126-0.05530.117229.1272-24.065992.3492
580.00150.00190.00310.0056-0.0008-0.0005-0.00340.01460.0119-0.00530.0087-0.0038-0.02070.00010.00750.1705-0.1314-0.14220.15770.02530.195225.4924-25.5837102.1773
590.0068-0.00540.00730.0039-0.00530.0122-0.0081-0.0025-0.00350.0107-0.02480.0111-0.0019-0.015-0.02150.1475-0.1173-0.05580.0949-0.05260.142229.6675-22.1817112.6823
600.0029-0.00170.00370.001-0.00180.0027-0.008-0.0075-0.00740.00130.0133-0.0070.00120.0334-0.00110.1623-0.1128-0.1260.2065-0.00580.203731.7463-36.3785112.9163
61-0.0001-0.00020.0002-0.00020-0.00020.0111-0.0035-0.00930.0052-0.0044-0.0078-0.0051-0.004900.8762-0.0559-0.02780.84210.03520.8357-1.2627-52.572752.2596
620.0002-0.00150.00210.0003-0.00010.0015-0.02550.0239-0.0126-0.015-0.01470.0040.0016-0.0294-00.53750.1098-0.07920.4675-0.01220.52040.2299-48.666540.8312
630.00020.0004-0.00010.0009-0.00080.00040.007-0.00820.0046-0.00080.0079-0.01210.0046-0.0007-00.32470.0785-0.00310.38190.0030.420416.0413-41.873953.4738
640.00020.00040.00160.0017-0.00170.0014-0.0249-0.0243-0.006-0.0218-0.05080.01510.0030.0492-0.00010.4149-0.0143-0.08070.39380.03020.48131.2673-47.333847.4781
65-0.0024-0.00190.00130.002-0.00160.001-0.01630.0257-0.01730.01190.0122-0.0041-0.00740.0032-00.31990.0486-0.05610.34550.01950.23226.4848-43.802840.5962
660.00050.00040.00030.00010.0002-0.0001-0.0070.0043-0.00310.0001-0.01830.00540.0036-0.009-00.3770.07490.02540.34620.04750.36281.1151-44.792760.0296
670.00060-0.00060.00060.00050.00050.003-0.00470.00690.00210.0046-0.00590.0023-0.006600.4032-0.03110.11920.4129-0.01930.4291-5.5989-37.507954.0776
680.00050.0006-0.00050.0005-0.0003-0.00010.00280.006-0.00150.0009-0.00320.0001-0.01780.000200.3029-0.04760.06730.37280.01480.38519.7697-37.158542.7678
690.0215-0.0007-0.02750.0573-0.03810.05340.05440.02320.0903-0.02570.0377-0.0225-0.0681-0.01550.15460.0730.0830.1830.08210.16280.227919.0134-12.487.3432
700.0007-0.0007-0.00110.00170.0019-0.00030.02110.00590.004-0.0003-0.02520.0180.03450.0151-0.00560.46040.00640.02920.09780.12520.30638.507512.8443-2.3856
710.00110.00110.001-0.0004-0.00010.00140.0210.0066-0.0042-0.0194-0.0003-0.01740.01320.005-00.58140.1406-0.02950.39510.07050.420120.4255-23.4574-11.8344
720.0026-0.00390.00240.0018-0.00450.002-0.0048-0.00330.0154-0.04930.0061-0.0251-0.0181-0.00360.00220.1964-0.01650.00230.01250.08340.258617.3974-11.3313-5.5001
730.0003-0.0031-0.00120.0042-0.00150.00040.06290.0137-0.0191-0.0169-0.0418-0.00310.0524-0.026-00.39950.04110.06470.24340.04570.34031.4955-26.6502-12.4817
740.0211-0.0094-0.0290.0170.01090.0347-0.01770.0338-0.00430.0301-0.0068-0.0227-0.02120.0198-0.00410.12250.07590.16930.05330.12710.101914.60611.3449-15.8491
750.0018-0.00040.00250.0007-0.00140.00270.03180.01640.00540.0127-0.0159-0.03660.0381-0.0017-00.49370.05190.06590.55570.05770.345110.9243-20.7455-16.7956
760.0063-0.00230.00070.0047-0.00530.0057-0.0075-0.0146-0.0046-0.02380.01140.0088-0.008-0.01860.00010.12570.0330.07050.2020.05580.035713.3053-11.5225-16.4099
770.0061-0.00110.00320.0045-0.00140.0018-0.0022-0.0050.01160.0327-0.0092-0.0090.01570.0016-0.03040.14210.01460.00960.01640.13420.15628.0129-4.0283-10.1493
780.0006-0.00040.00020.0007-0.00050.00050.0025-0.0010.0005-0.00020.0007-0.00320.0010.0002-01.3339-0.01-0.0021.32520.02031.3234-8.2656-15.57723.4601
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1700.00150.0008-0.00760.0029-0.00570.0371-0.00960.0021-00.0061-0.00120.00210.00070.0007-0.00010.41350.0508-0.00170.4155-0.01520.411147.2571-128.1673133.6694
1710.00030.0002-0.00050.0008-0.00280.00130.01650.0010.0150.00290.0013-0.0071-0.0118-0.002-00.5418-0.09340.04940.30380.19320.401268.4416-99.1704155.3148
1720.00660.0018-0.00530.00330.00150.0063-0.00210.01040.0107-0.00790.0009-0.0109-0.02560.00360.00320.1139-0.0071-0.08330.10830.18020.186868.3129-111.2728151.4078
1730.0077-0.00820.00580.0083-0.00670.0120.001-0.0096-0.0018-0.00850.0143-0.0012-0.00530.0060.00340.23590.00820.0740.0607-0.03660.070456.1882-111.0358140.8765
1740.0002-0.001-0.00020.0008-0.00020.0001-0.00770.01480.00570.0129-0.00040.0048-0.0091-0.004-00.77880.0242-0.02270.75040.06310.776945.3604-96.6128143.3884
1750.02060.0026-0.01290.02290.01360.01910.0080.0151-0.0065-0.00720.0035-0.0119-0.0116-0.01850.00870.2619-0.18270.02050.1458-0.07940.288352.7693-95.7699165.2193
176-0.00080.000200.00050.00090.0003-0.0055-0.0243-0.00110.0048-0.003-0.00760.0010.0133-00.4490.0064-0.00470.50040.00870.470974.6909-113.1776171.5111
1770.0032-0.00530.00960.03350.00260.0241-0.0216-0.0105-0.0296-0.0247-0.0370.00010.01450.0242-0.04910.1493-0.0807-0.0060.0920.0810.145657.2969-128.3582154.4314
1780.00020.0001-00.00060.0001-00.04760.0120.00580.00240.0033-0.0454-0.0391-0.042400.4951-0.0641-0.05050.40870.03720.340958.9462-101.8053160.2865
1790.0010.0074-0.00020.0125-0.01070.0046-0.0051-0.0205-0.00720.0302-0.01-0.0199-0.01530.0358-0.0040.2615-0.1656-0.05430.05330.15430.107659.6665-114.6662157.6303
1800.000300.00010-00.00020.00090.0020.00060.0026-0.0003-0.00020.0004-0.003200.62950.0312-0.01210.67140.02780.618839.9222-107.9556140.5174
1810.0007-0.00020.00060.0001-0.00060.00050.0023-0.00130.00060.0096-0.0012-0.00190.00130.004700.36710.0371-0.10930.37650.03230.366733.774-103.1134151.0601
1820.0033-0.0008-0.00410.00520.00120.0059-0.05590.0325-0.03290.0233-0.00290.03580.050.0249-0.00010.2817-0.20510.05140.58840.05170.5507-22.0934-120.5652218.6815
1830.0481-0.00630.00410.1564-0.0610.0270.02210.0481-0.0370.1186-0.1367-0.0948-0.0767-0.1723-0.09590.3975-0.0913-0.42230.56490.01610.3974-17.2364-102.3491217.3304
1840.01640.00520.01410.0030.00530.013-0.04020.015-0.02630.0058-0.02540.03630.0049-0.075-0.0030.46650.0706-0.13410.5118-0.10730.2009-32.9681-91.6871223.0015
1850.0014-0.00140.0004-0.00060.00050.0002-0.0006-0.00260.0015-0.00060.0030.00930.0033-0.0064-00.51610.0267-0.00320.61820.05170.5572-46.7255-100.5715214.8801
186-0.0007-0.00020.00040.0002-0.00130.0019-0.0135-0.0092-0.0039-0.0033-0.0201-0.0131-0.00720.010600.9775-0.04940.08111.07660.00720.9023-22.7113-98.783241.7769
1870.0023-0.00020.0008-0.00350.00030.00220.030.01010.0251-0.0260.00130.083-0.0123-0.014500.7660.057-0.08960.83510.04270.6636-32.0356-79.6822218.316
1880.01590.00910.01690.00860.00390.0429-0.0226-0.03810.0335-0.0585-0.0243-0.0116-0.0398-0.0994-0.04340.30270.0041-0.07720.0104-0.11530.22922.5016-98.4577175.7073
1890.00440.0045-0.00120.0012-0.0013-0.0001-0.0619-0.0299-0.0244-0.0006-0.04860.0433-0.00110.0485-00.3991-0.0330.050.39690.03710.53256.2707-132.2767193.6409
1900.0412-0.0017-0.02780.05090.03470.0489-0.0766-0.0472-0.10440.0344-0.05570.0510.02430.0198-0.1890.1331-0.2139-0.1570.20710.18640.325212.9632-113.5629193.4115
1910.01650.0071-0.01460.0076-0.01270.0150.02510.0504-0.0174-0.0511-0.02120.0876-0.0461-0.1093-0.00010.44230.0041-0.15550.41940.09270.3544-6.8187-110.0011199.2647
1920.00240.0048-0.00260.0111-0.01290.0091-0.0453-0.0049-0.04680.039-0.04920.0149-0.0102-0.0368-0.00010.4872-0.0189-0.09950.64190.0360.6302-5.6304-120.0642202.6995
1930.0025-0.00130.00070.0018-0.00140.0006-0.0107-0.040.0272-0.00960.00770.00460.0003-0.0092-00.2959-0.08350.09490.24090.16630.559340.6673-139.8025154.3592
1940.00090.00120.00220.0037-0.0005-0.0002-0.0358-0.01060.0067-0.0226-0.03230.01470.01230.00980.00010.4273-0.0731-0.0280.3010.09830.550542.7636-135.2185169.6361
1950.03820.0329-0.01380.0411-0.0120.0537-0.06160.05730.0229-0.01240.0083-0.02970.0131-0.0488-0.06440.3004-0.1332-0.00750.11750.2120.446142.3671-126.1834156.3281
1960.01030.0027-0.00220.0095-0.01060.0057-0.01370.0026-0.00060.0345-0.02810.0219-0.05650.0385-0.01630.3355-0.1072-0.26380.08230.18180.253545.6081-115.4904166.0283
1970.030.0107-0.01840.0045-0.00410.02640.07810.1172-0.05550.0608-0.01890.0536-0.0075-0.1907-0.00330.1604-0.0198-0.0650.09710.08890.489927.6487-119.2296172.4889
1980.02730.02210.00740.015-0.00130.00350.04180.0222-0.03670.04050.01820.0144-0.0245-0.0060.05820.2380.1509-0.09980.25790.11750.375821.9307-124.1966171.8872
1990.0569-0.01010.01150.0073-0.00290.0070.016-0.0767-0.04950.0112-0.0803-0.00040.04130.0751-0.05410.090.0725-0.14370.30260.25780.349682.1252-110.0144126.9543
2000.0411-0.0090.0080.0496-0.03650.0192-0.009-0.1864-0.083-0.0089-0.1082-0.06850.12390.1396-0.12390.39530.006-0.04830.24880.32490.25476.5316-121.9475132.8434
2010.00810.0017-0.0090.0059-0.00890.0084-0.02670.02780.00190.02420.0232-0.00240.0426-0.0235-0.03210.25030.09980.02180.12670.22140.281368.4621-138.5695134.749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain '1' and (resid 2 through 38 )
2X-RAY DIFFRACTION2chain '1' and (resid 39 through 60 )
3X-RAY DIFFRACTION3chain '1' and (resid 61 through 86 )
4X-RAY DIFFRACTION4chain '1' and (resid 87 through 155 )
5X-RAY DIFFRACTION5chain '1' and (resid 156 through 232 )
6X-RAY DIFFRACTION6chain '1' and (resid 233 through 366 )
7X-RAY DIFFRACTION7chain '1' and (resid 367 through 438 )
8X-RAY DIFFRACTION8chain '2' and (resid 3 through 22 )
9X-RAY DIFFRACTION9chain '2' and (resid 23 through 38 )
10X-RAY DIFFRACTION10chain '2' and (resid 39 through 66 )
11X-RAY DIFFRACTION11chain '2' and (resid 67 through 77 )
12X-RAY DIFFRACTION12chain '2' and (resid 78 through 92 )
13X-RAY DIFFRACTION13chain '2' and (resid 93 through 104 )
14X-RAY DIFFRACTION14chain '2' and (resid 105 through 116 )
15X-RAY DIFFRACTION15chain '2' and (resid 117 through 132 )
16X-RAY DIFFRACTION16chain '2' and (resid 133 through 146 )
17X-RAY DIFFRACTION17chain '2' and (resid 147 through 158 )
18X-RAY DIFFRACTION18chain '2' and (resid 159 through 165 )
19X-RAY DIFFRACTION19chain '2' and (resid 166 through 180 )
20X-RAY DIFFRACTION20chain '3' and (resid 1 through 137 )
21X-RAY DIFFRACTION21chain '3' and (resid 138 through 193 )
22X-RAY DIFFRACTION22chain '3' and (resid 194 through 309 )
23X-RAY DIFFRACTION23chain '3' and (resid 310 through 350 )
24X-RAY DIFFRACTION24chain '3' and (resid 351 through 460 )
25X-RAY DIFFRACTION25chain '3' and (resid 461 through 595 )
26X-RAY DIFFRACTION26chain '3' and (resid 596 through 667 )
27X-RAY DIFFRACTION27chain '3' and (resid 668 through 719 )
28X-RAY DIFFRACTION28chain '3' and (resid 720 through 777 )
29X-RAY DIFFRACTION29chain '4' and (resid 26 through 139 )
30X-RAY DIFFRACTION30chain '4' and (resid 140 through 208 )
31X-RAY DIFFRACTION31chain '4' and (resid 209 through 247 )
32X-RAY DIFFRACTION32chain '4' and (resid 248 through 409 )
33X-RAY DIFFRACTION33chain '5' and (resid 1 through 13 )
34X-RAY DIFFRACTION34chain '5' and (resid 14 through 31 )
35X-RAY DIFFRACTION35chain '5' and (resid 32 through 43 )
36X-RAY DIFFRACTION36chain '5' and (resid 44 through 67 )
37X-RAY DIFFRACTION37chain '5' and (resid 68 through 86 )
38X-RAY DIFFRACTION38chain '5' and (resid 87 through 109 )
39X-RAY DIFFRACTION39chain '5' and (resid 110 through 121 )
40X-RAY DIFFRACTION40chain '5' and (resid 122 through 141 )
41X-RAY DIFFRACTION41chain '5' and (resid 142 through 175 )
42X-RAY DIFFRACTION42chain '5' and (resid 176 through 185 )
43X-RAY DIFFRACTION43chain '5' and (resid 186 through 196 )
44X-RAY DIFFRACTION44chain '6' and (resid 20 through 34 )
45X-RAY DIFFRACTION45chain '6' and (resid 35 through 56 )
46X-RAY DIFFRACTION46chain '6' and (resid 57 through 77 )
47X-RAY DIFFRACTION47chain '6' and (resid 78 through 181 )
48X-RAY DIFFRACTION48chain '9' and (resid 2 through 18 )
49X-RAY DIFFRACTION49chain '9' and (resid 19 through 38 )
50X-RAY DIFFRACTION50chain '9' and (resid 39 through 48 )
51X-RAY DIFFRACTION51chain '9' and (resid 49 through 74 )
52X-RAY DIFFRACTION52chain '9' and (resid 75 through 112 )
53X-RAY DIFFRACTION53chain '9' and (resid 113 through 135 )
54X-RAY DIFFRACTION54chain '9' and (resid 136 through 167 )
55X-RAY DIFFRACTION55chain '9' and (resid 168 through 181 )
56X-RAY DIFFRACTION56chain '7' and (resid 3 through 27 )
57X-RAY DIFFRACTION57chain '7' and (resid 28 through 60 )
58X-RAY DIFFRACTION58chain '7' and (resid 61 through 81 )
59X-RAY DIFFRACTION59chain '7' and (resid 82 through 111 )
60X-RAY DIFFRACTION60chain '7' and (resid 112 through 129 )
61X-RAY DIFFRACTION61chain 'W' and (resid 1 through 9 )
62X-RAY DIFFRACTION62chain 'W' and (resid 10 through 35 )
63X-RAY DIFFRACTION63chain 'W' and (resid 36 through 46 )
64X-RAY DIFFRACTION64chain 'W' and (resid 47 through 69 )
65X-RAY DIFFRACTION65chain 'W' and (resid 70 through 95 )
66X-RAY DIFFRACTION66chain 'W' and (resid 96 through 106 )
67X-RAY DIFFRACTION67chain 'W' and (resid 107 through 117 )
68X-RAY DIFFRACTION68chain 'W' and (resid 118 through 127 )
69X-RAY DIFFRACTION69chain 'A' and (resid 2 through 88 )
70X-RAY DIFFRACTION70chain 'A' and (resid 89 through 117 )
71X-RAY DIFFRACTION71chain 'J' and (resid 1 through 24 )
72X-RAY DIFFRACTION72chain 'J' and (resid 25 through 73 )
73X-RAY DIFFRACTION73chain 'J' and (resid 74 through 108 )
74X-RAY DIFFRACTION74chain 'J' and (resid 109 through 160 )
75X-RAY DIFFRACTION75chain 'K' and (resid 1 through 23 )
76X-RAY DIFFRACTION76chain 'K' and (resid 24 through 51 )
77X-RAY DIFFRACTION77chain 'K' and (resid 52 through 78 )
78X-RAY DIFFRACTION78chain 'K' and (resid 79 through 86 )
79X-RAY DIFFRACTION79chain 'K' and (resid 87 through 95 )
80X-RAY DIFFRACTION80chain 'L' and (resid 1 through 70 )
81X-RAY DIFFRACTION81chain 'L' and (resid 71 through 425 )
82X-RAY DIFFRACTION82chain 'L' and (resid 426 through 458 )
83X-RAY DIFFRACTION83chain 'L' and (resid 459 through 510 )
84X-RAY DIFFRACTION84chain 'L' and (resid 511 through 542 )
85X-RAY DIFFRACTION85chain 'L' and (resid 543 through 605 )
86X-RAY DIFFRACTION86chain 'M' and (resid 1 through 114 )
87X-RAY DIFFRACTION87chain 'M' and (resid 115 through 414 )
88X-RAY DIFFRACTION88chain 'M' and (resid 415 through 467 )
89X-RAY DIFFRACTION89chain 'N' and (resid 1 through 127 )
90X-RAY DIFFRACTION90chain 'N' and (resid 128 through 187 )
91X-RAY DIFFRACTION91chain 'N' and (resid 188 through 357 )
92X-RAY DIFFRACTION92chain 'N' and (resid 358 through 395 )
93X-RAY DIFFRACTION93chain 'N' and (resid 396 through 427 )
94X-RAY DIFFRACTION94chain 'H' and (resid 2 through 42 )
95X-RAY DIFFRACTION95chain 'H' and (resid 43 through 104 )
96X-RAY DIFFRACTION96chain 'H' and (resid 105 through 147 )
97X-RAY DIFFRACTION97chain 'H' and (resid 148 through 262 )
98X-RAY DIFFRACTION98chain 'H' and (resid 263 through 296 )
99X-RAY DIFFRACTION99chain 'H' and (resid 297 through 334 )
100X-RAY DIFFRACTION100chain 'H' and (resid 335 through 354 )
101X-RAY DIFFRACTION101chain 'B' and (resid 2 through 38 )
102X-RAY DIFFRACTION102chain 'B' and (resid 39 through 60 )
103X-RAY DIFFRACTION103chain 'B' and (resid 61 through 124 )
104X-RAY DIFFRACTION104chain 'B' and (resid 125 through 267 )
105X-RAY DIFFRACTION105chain 'B' and (resid 268 through 366 )
106X-RAY DIFFRACTION106chain 'B' and (resid 367 through 395 )
107X-RAY DIFFRACTION107chain 'B' and (resid 396 through 438 )
108X-RAY DIFFRACTION108chain 'C' and (resid 3 through 22 )
109X-RAY DIFFRACTION109chain 'C' and (resid 23 through 38 )
110X-RAY DIFFRACTION110chain 'C' and (resid 39 through 53 )
111X-RAY DIFFRACTION111chain 'C' and (resid 54 through 66 )
112X-RAY DIFFRACTION112chain 'C' and (resid 67 through 77 )
113X-RAY DIFFRACTION113chain 'C' and (resid 78 through 92 )
114X-RAY DIFFRACTION114chain 'C' and (resid 93 through 104 )
115X-RAY DIFFRACTION115chain 'C' and (resid 105 through 116 )
116X-RAY DIFFRACTION116chain 'C' and (resid 117 through 146 )
117X-RAY DIFFRACTION117chain 'C' and (resid 147 through 158 )
118X-RAY DIFFRACTION118chain 'C' and (resid 159 through 180 )
119X-RAY DIFFRACTION119chain 'D' and (resid 1 through 128 )
120X-RAY DIFFRACTION120chain 'D' and (resid 129 through 193 )
121X-RAY DIFFRACTION121chain 'D' and (resid 194 through 309 )
122X-RAY DIFFRACTION122chain 'D' and (resid 310 through 350 )
123X-RAY DIFFRACTION123chain 'D' and (resid 351 through 546 )
124X-RAY DIFFRACTION124chain 'D' and (resid 547 through 594 )
125X-RAY DIFFRACTION125chain 'D' and (resid 595 through 667 )
126X-RAY DIFFRACTION126chain 'D' and (resid 668 through 719 )
127X-RAY DIFFRACTION127chain 'D' and (resid 720 through 777 )
128X-RAY DIFFRACTION128chain 'E' and (resid 26 through 53 )
129X-RAY DIFFRACTION129chain 'E' and (resid 54 through 139 )
130X-RAY DIFFRACTION130chain 'E' and (resid 140 through 208 )
131X-RAY DIFFRACTION131chain 'E' and (resid 209 through 232 )
132X-RAY DIFFRACTION132chain 'E' and (resid 233 through 409 )
133X-RAY DIFFRACTION133chain 'F' and (resid 1 through 13 )
134X-RAY DIFFRACTION134chain 'F' and (resid 14 through 31 )
135X-RAY DIFFRACTION135chain 'F' and (resid 32 through 86 )
136X-RAY DIFFRACTION136chain 'F' and (resid 87 through 121 )
137X-RAY DIFFRACTION137chain 'F' and (resid 122 through 175 )
138X-RAY DIFFRACTION138chain 'F' and (resid 176 through 196 )
139X-RAY DIFFRACTION139chain 'G' and (resid 20 through 34 )
140X-RAY DIFFRACTION140chain 'G' and (resid 35 through 56 )
141X-RAY DIFFRACTION141chain 'G' and (resid 57 through 88 )
142X-RAY DIFFRACTION142chain 'G' and (resid 89 through 158 )
143X-RAY DIFFRACTION143chain 'G' and (resid 159 through 168 )
144X-RAY DIFFRACTION144chain 'G' and (resid 169 through 181 )
145X-RAY DIFFRACTION145chain 'O' and (resid 2 through 18 )
146X-RAY DIFFRACTION146chain 'O' and (resid 19 through 30 )
147X-RAY DIFFRACTION147chain 'O' and (resid 31 through 48 )
148X-RAY DIFFRACTION148chain 'O' and (resid 49 through 74 )
149X-RAY DIFFRACTION149chain 'O' and (resid 75 through 112 )
150X-RAY DIFFRACTION150chain 'O' and (resid 113 through 125 )
151X-RAY DIFFRACTION151chain 'O' and (resid 126 through 168 )
152X-RAY DIFFRACTION152chain 'O' and (resid 169 through 181 )
153X-RAY DIFFRACTION153chain 'I' and (resid 3 through 27 )
154X-RAY DIFFRACTION154chain 'I' and (resid 28 through 60 )
155X-RAY DIFFRACTION155chain 'I' and (resid 61 through 81 )
156X-RAY DIFFRACTION156chain 'I' and (resid 82 through 111 )
157X-RAY DIFFRACTION157chain 'I' and (resid 112 through 129 )
158X-RAY DIFFRACTION158chain 'X' and (resid 1 through 9 )
159X-RAY DIFFRACTION159chain 'X' and (resid 10 through 21 )
160X-RAY DIFFRACTION160chain 'X' and (resid 22 through 29 )
161X-RAY DIFFRACTION161chain 'X' and (resid 30 through 46 )
162X-RAY DIFFRACTION162chain 'X' and (resid 47 through 59 )
163X-RAY DIFFRACTION163chain 'X' and (resid 60 through 83 )
164X-RAY DIFFRACTION164chain 'X' and (resid 84 through 93 )
165X-RAY DIFFRACTION165chain 'X' and (resid 94 through 106 )
166X-RAY DIFFRACTION166chain 'X' and (resid 107 through 127 )
167X-RAY DIFFRACTION167chain 'P' and (resid 2 through 58 )
168X-RAY DIFFRACTION168chain 'P' and (resid 59 through 83 )
169X-RAY DIFFRACTION169chain 'P' and (resid 84 through 112 )
170X-RAY DIFFRACTION170chain 'P' and (resid 113 through 117 )
171X-RAY DIFFRACTION171chain 'R' and (resid 1 through 24 )
172X-RAY DIFFRACTION172chain 'R' and (resid 25 through 62 )
173X-RAY DIFFRACTION173chain 'R' and (resid 63 through 73 )
174X-RAY DIFFRACTION174chain 'R' and (resid 74 through 87 )
175X-RAY DIFFRACTION175chain 'R' and (resid 88 through 108 )
176X-RAY DIFFRACTION176chain 'R' and (resid 109 through 123 )
177X-RAY DIFFRACTION177chain 'R' and (resid 124 through 160 )
178X-RAY DIFFRACTION178chain 'S' and (resid 1 through 23 )
179X-RAY DIFFRACTION179chain 'S' and (resid 24 through 76 )
180X-RAY DIFFRACTION180chain 'S' and (resid 77 through 86 )
181X-RAY DIFFRACTION181chain 'S' and (resid 87 through 95 )
182X-RAY DIFFRACTION182chain 'T' and (resid 1 through 70 )
183X-RAY DIFFRACTION183chain 'T' and (resid 71 through 290 )
184X-RAY DIFFRACTION184chain 'T' and (resid 291 through 425 )
185X-RAY DIFFRACTION185chain 'T' and (resid 426 through 455 )
186X-RAY DIFFRACTION186chain 'T' and (resid 456 through 488 )
187X-RAY DIFFRACTION187chain 'T' and (resid 489 through 542 )
188X-RAY DIFFRACTION188chain 'T' and (resid 543 through 605 )
189X-RAY DIFFRACTION189chain 'U' and (resid 1 through 95 )
190X-RAY DIFFRACTION190chain 'U' and (resid 96 through 304 )
191X-RAY DIFFRACTION191chain 'U' and (resid 305 through 414 )
192X-RAY DIFFRACTION192chain 'U' and (resid 415 through 467 )
193X-RAY DIFFRACTION193chain 'V' and (resid 1 through 42 )
194X-RAY DIFFRACTION194chain 'V' and (resid 43 through 75 )
195X-RAY DIFFRACTION195chain 'V' and (resid 76 through 127 )
196X-RAY DIFFRACTION196chain 'V' and (resid 128 through 225 )
197X-RAY DIFFRACTION197chain 'V' and (resid 226 through 357 )
198X-RAY DIFFRACTION198chain 'V' and (resid 358 through 427 )
199X-RAY DIFFRACTION199chain 'Q' and (resid 2 through 104 )
200X-RAY DIFFRACTION200chain 'Q' and (resid 105 through 296 )
201X-RAY DIFFRACTION201chain 'Q' and (resid 297 through 354 )

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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