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Basic information

Entry
Database: PDB / ID: 3ias
TitleCrystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution
Components(NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 8
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / RESPIRATORY CHAIN
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) activity / respiratory chain complex I / molybdopterin cofactor binding / iron-sulfur cluster assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding / 2 iron, 2 sulfur cluster binding ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) activity / respiratory chain complex I / molybdopterin cofactor binding / 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-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 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily ...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 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / 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) / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 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 dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / 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. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / 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. / 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 / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Helix non-globular / Special / Glutaredoxin / Glutaredoxin / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / Roll / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / 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 15
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsSazanov, L.A. / Berrisford, J.M.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Structural basis for the mechanism of respiratory complex I
Authors: Berrisford, J.M. / Sazanov, L.A.
#1: Journal: Science / Year: 2006
Title: Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
Authors: Sazanov, L.A. / Hinchliffe, P.
History
DepositionJul 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
A: NADH-quinone oxidoreductase subunit 1
B: NADH-quinone oxidoreductase subunit 2
C: NADH-quinone oxidoreductase subunit 3
D: NADH-quinone oxidoreductase subunit 4
E: NADH-quinone oxidoreductase subunit 5
F: NADH-quinone oxidoreductase subunit 6
G: NADH-quinone oxidoreductase subunit 9
H: NADH-quinone oxidoreductase subunit 15
J: NADH-quinone oxidoreductase subunit 1
K: NADH-quinone oxidoreductase subunit 2
L: NADH-quinone oxidoreductase subunit 3
M: NADH-quinone oxidoreductase subunit 4
N: NADH-quinone oxidoreductase subunit 5
O: NADH-quinone oxidoreductase subunit 6
P: NADH-quinone oxidoreductase subunit 9
Q: NADH-quinone oxidoreductase subunit 15
S: NADH-quinone oxidoreductase subunit 1
T: NADH-quinone oxidoreductase subunit 2
U: NADH-quinone oxidoreductase subunit 3
V: NADH-quinone oxidoreductase subunit 4
W: NADH-quinone oxidoreductase subunit 5
X: NADH-quinone oxidoreductase subunit 6
Y: NADH-quinone oxidoreductase subunit 9
Z: NADH-quinone oxidoreductase subunit 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,138,36488
Polymers1,124,64532
Non-polymers13,71956
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,59122
Polymers281,1618
Non-polymers3,43014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NADH-quinone oxidoreductase subunit 1
B: NADH-quinone oxidoreductase subunit 2
C: NADH-quinone oxidoreductase subunit 3
D: NADH-quinone oxidoreductase subunit 4
E: NADH-quinone oxidoreductase subunit 5
F: NADH-quinone oxidoreductase subunit 6
G: NADH-quinone oxidoreductase subunit 9
H: NADH-quinone oxidoreductase subunit 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,59122
Polymers281,1618
Non-polymers3,43014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: NADH-quinone oxidoreductase subunit 1
K: NADH-quinone oxidoreductase subunit 2
L: NADH-quinone oxidoreductase subunit 3
M: NADH-quinone oxidoreductase subunit 4
N: NADH-quinone oxidoreductase subunit 5
O: NADH-quinone oxidoreductase subunit 6
P: NADH-quinone oxidoreductase subunit 9
Q: NADH-quinone oxidoreductase subunit 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,59122
Polymers281,1618
Non-polymers3,43014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
S: NADH-quinone oxidoreductase subunit 1
T: NADH-quinone oxidoreductase subunit 2
U: NADH-quinone oxidoreductase subunit 3
V: NADH-quinone oxidoreductase subunit 4
W: NADH-quinone oxidoreductase subunit 5
X: NADH-quinone oxidoreductase subunit 6
Y: NADH-quinone oxidoreductase subunit 9
Z: NADH-quinone oxidoreductase subunit 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,59122
Polymers281,1618
Non-polymers3,43014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.080, 266.112, 201.731
Angle α, β, γ (deg.)90.000, 104.710, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
113
21C
31L
41U
121
22A
32J
42S
134
23D
33M
43V
145
24E
34N
44W
152
25B
35K
45T
169
26G
36P
46Y
176
27F
37O
47X
187
28H
38Q
48Z

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPROPROchain 3 and (resseq 1:55 or resseq 73:143 or resseq 150:777 )3C1 - 551 - 55
121ILEILETYRTYRchain 3 and (resseq 1:55 or resseq 73:143 or resseq 150:777 )3C73 - 14373 - 143
131GLUGLUVALVALchain 3 and (resseq 1:55 or resseq 73:143 or resseq 150:777 )3C150 - 777150 - 777
211METMETPROPROchain C and (resseq 1:55 or resseq 73:143 or resseq 150:777 )CK1 - 551 - 55
221ILEILETYRTYRchain C and (resseq 1:55 or resseq 73:143 or resseq 150:777 )CK73 - 14373 - 143
231GLUGLUVALVALchain C and (resseq 1:55 or resseq 73:143 or resseq 150:777 )CK150 - 777150 - 777
311METMETPROPROchain L and (resseq 1:55 or resseq 73:143 or resseq 150:777 )LS1 - 551 - 55
321ILEILETYRTYRchain L and (resseq 1:55 or resseq 73:143 or resseq 150:777 )LS73 - 14373 - 143
331GLUGLUVALVALchain L and (resseq 1:55 or resseq 73:143 or resseq 150:777 )LS150 - 777150 - 777
411METMETPROPROchain U and (resseq 1:55 or resseq 73:143 or resseq 150:777 )UAA1 - 551 - 55
421ILEILETYRTYRchain U and (resseq 1:55 or resseq 73:143 or resseq 150:777 )UAA73 - 14373 - 143
431GLUGLUVALVALchain U and (resseq 1:55 or resseq 73:143 or resseq 150:777 )UAA150 - 777150 - 777
112THRTHRARGARGchain 1 and (resseq 2:438 )1A2 - 4382 - 438
212THRTHRARGARGchain A and (resseq 2:438 )AI2 - 4382 - 438
312THRTHRARGARGchain J and (resseq 2:438 )JQ2 - 4382 - 438
412THRTHRARGARGchain S and (resseq 2:438 )SY2 - 4382 - 438
113METMETGLYGLYchain 4 and (resseq 26:31 or resseq 39:409 )4D26 - 3126 - 31
123GLYGLYARGARGchain 4 and (resseq 26:31 or resseq 39:409 )4D39 - 40939 - 409
213METMETGLYGLYchain D and (resseq 26:31 or resseq 39:409 )DL26 - 3126 - 31
223GLYGLYARGARGchain D and (resseq 26:31 or resseq 39:409 )DL39 - 40939 - 409
313METMETGLYGLYchain M and (resseq 26:31 or resseq 39:409 )MT26 - 3126 - 31
323GLYGLYARGARGchain M and (resseq 26:31 or resseq 39:409 )MT39 - 40939 - 409
413METMETGLYGLYchain V and (resseq 26:31 or resseq 39:409 )VBA26 - 3126 - 31
423GLYGLYARGARGchain V and (resseq 26:31 or resseq 39:409 )VBA39 - 40939 - 409
114METMETTRPTRPchain 5 and (resseq 1:196 )5E1 - 1961 - 196
214METMETTRPTRPchain E and (resseq 1:196 )EM1 - 1961 - 196
314METMETTRPTRPchain N and (resseq 1:196 )NU1 - 1961 - 196
414METMETTRPTRPchain W and (resseq 1:196 )WCA1 - 1961 - 196
115PHEPHEGLUGLUchain 2 and (resseq 3:180 )2B3 - 1803 - 180
215PHEPHEGLUGLUchain B and (resseq 3:180 )BJ3 - 1803 - 180
315PHEPHEGLUGLUchain K and (resseq 3:180 )KR3 - 1803 - 180
415PHEPHEGLUGLUchain T and (resseq 3:180 )TZ3 - 1803 - 180
116TYRTYRGLYGLYchain 9 and (resseq 26:179 )9G26 - 17926 - 179
216TYRTYRGLYGLYchain G and (resseq 26:179 )GO26 - 17926 - 179
316TYRTYRGLYGLYchain P and (resseq 26:179 )PW26 - 17926 - 179
416TYRTYRGLYGLYchain Y and (resseq 26:179 )YEA26 - 17926 - 179
117GLUGLUARGARGchain 6 and (resseq 15:57 or resseq 74:175 )6F15 - 5715 - 57
127GLNGLNALAALAchain 6 and (resseq 15:57 or resseq 74:175 )6F74 - 17574 - 175
217GLUGLUARGARGchain F and (resseq 15:57 or resseq 74:175 )FN15 - 5715 - 57
227GLNGLNALAALAchain F and (resseq 15:57 or resseq 74:175 )FN74 - 17574 - 175
317GLUGLUARGARGchain O and (resseq 15:57 or resseq 74:175 )OV15 - 5715 - 57
327GLNGLNALAALAchain O and (resseq 15:57 or resseq 74:175 )OV74 - 17574 - 175
417GLUGLUARGARGchain X and (resseq 15:57 or resseq 74:175 )XDA15 - 5715 - 57
427GLNGLNALAALAchain X and (resseq 15:57 or resseq 74:175 )XDA74 - 17574 - 175
118ALAALAALAALAchain 7 and (resseq 3:129 )7H3 - 1293 - 129
218ALAALAALAALAchain H and (resseq 3:129 )HP3 - 1293 - 129
318ALAALAALAALAchain Q and (resseq 3:129 )QX3 - 1293 - 129
418ALAALAALAALAchain Z and (resseq 3:129 )ZFA3 - 1293 - 129

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

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NADH-quinone oxidoreductase subunit ... , 8 types, 32 molecules 1AJS2BKT3CLU4DMV5ENW6FOX9GPY7HQZ

#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.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56222, NADH dehydrogenase (quinone)
#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.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56221, NADH dehydrogenase (quinone)
#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.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56223, NADH dehydrogenase (quinone)
#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.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56220, NADH dehydrogenase (quinone)
#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.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56219, NADH dehydrogenase (quinone)
#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.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56218, NADH dehydrogenase (quinone)
#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.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56224, NADH dehydrogenase (quinone)
#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.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SKZ7, NADH dehydrogenase (quinone)

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Non-polymers , 4 types, 56 molecules

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


Mass: 351.640 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#11: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#12: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.4 M NaCl, 0.1 M CaCl2, 8% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97564 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2004
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97564 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. all: 218122 / Num. obs: 218122 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 69.08 Å2 / Rmerge(I) obs: 0.18 / Rsym value: 0.18 / Net I/σ(I): 6
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.2 / Num. unique all: 30663 / Rsym value: 0.759 / % possible all: 89

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FUG

2fug


Resolution: 3.15→29.985 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.793 / SU ML: 0.55 / Isotropic thermal model: Isotropic restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 28.34 / Stereochemistry target values: MLHL
Details: Native structure factors were anisotropically scaled and truncated to resolution limits of 3.15, 3.15 and 3.5 angstrom along a*, b* and c*, respectively. HL coefficients are from phasing run ...Details: Native structure factors were anisotropically scaled and truncated to resolution limits of 3.15, 3.15 and 3.5 angstrom along a*, b* and c*, respectively. HL coefficients are from phasing run in SHARP on native, Fe-peak and two derivative datasets, described previously (PDB 2FUG)
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3881 1.99 %RANDOM
Rwork0.237 ---
all0.238 195404 --
obs0.238 195404 82.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.61 Å2 / ksol: 0.282 e/Å3
Displacement parametersBiso max: 157.46 Å2 / Biso mean: 72.78 Å2 / Biso min: 1.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.038 Å2-0 Å2-0.079 Å2
2---2.941 Å2-0 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 3.15→29.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms74632 0 396 0 75028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00877184
X-RAY DIFFRACTIONf_angle_d1.295105216
X-RAY DIFFRACTIONf_chiral_restr0.0911308
X-RAY DIFFRACTIONf_plane_restr0.00613596
X-RAY DIFFRACTIONf_dihedral_angle_d21.69128672
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
1135881X-RAY DIFFRACTIONPOSITIONAL0.035
12C5881X-RAY DIFFRACTIONPOSITIONAL0.035
13L5881X-RAY DIFFRACTIONPOSITIONAL0.033
14U5881X-RAY DIFFRACTIONPOSITIONAL0.034
2113417X-RAY DIFFRACTIONPOSITIONAL0.038
22A3417X-RAY DIFFRACTIONPOSITIONAL0.038
23J3417X-RAY DIFFRACTIONPOSITIONAL0.034
24S3417X-RAY DIFFRACTIONPOSITIONAL0.036
3143011X-RAY DIFFRACTIONPOSITIONAL0.033
32D3011X-RAY DIFFRACTIONPOSITIONAL0.033
33M3011X-RAY DIFFRACTIONPOSITIONAL0.032
34V3011X-RAY DIFFRACTIONPOSITIONAL0.035
4151608X-RAY DIFFRACTIONPOSITIONAL0.031
42E1608X-RAY DIFFRACTIONPOSITIONAL0.031
43N1608X-RAY DIFFRACTIONPOSITIONAL0.032
44W1608X-RAY DIFFRACTIONPOSITIONAL0.031
5121407X-RAY DIFFRACTIONPOSITIONAL0.035
52B1407X-RAY DIFFRACTIONPOSITIONAL0.035
53K1407X-RAY DIFFRACTIONPOSITIONAL0.032
54T1407X-RAY DIFFRACTIONPOSITIONAL0.035
6191194X-RAY DIFFRACTIONPOSITIONAL0.039
62G1194X-RAY DIFFRACTIONPOSITIONAL0.039
63P1194X-RAY DIFFRACTIONPOSITIONAL0.037
64Y1194X-RAY DIFFRACTIONPOSITIONAL0.039
7161114X-RAY DIFFRACTIONPOSITIONAL0.036
72F1114X-RAY DIFFRACTIONPOSITIONAL0.036
73O1114X-RAY DIFFRACTIONPOSITIONAL0.032
74X1114X-RAY DIFFRACTIONPOSITIONAL0.038
8171031X-RAY DIFFRACTIONPOSITIONAL0.033
82H1031X-RAY DIFFRACTIONPOSITIONAL0.033
83Q1031X-RAY DIFFRACTIONPOSITIONAL0.032
84Z1031X-RAY DIFFRACTIONPOSITIONAL0.035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3.15-3.3160.3782830.36314520148031452044
3.316-3.5230.364520.34323022234742302270
3.523-3.7950.3465620.31429146297082914688
3.795-4.1760.2976180.26230623312413062392
4.176-4.7780.2586700.22631243319133124394
4.778-6.0120.2296750.18831635323103163595
6.012-29.9870.2046210.16931334319553133494

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