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Entry
Database: PDB / ID: 3iam
TitleCrystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/ASU, with bound NADH
Components(NADH-quinone oxidoreductase subunit ...) 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) (non-electrogenic) activity / molybdopterin cofactor binding / iron-sulfur cluster assembly / electron transport coupled proton transport / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / molybdopterin cofactor binding / iron-sulfur cluster assembly / electron transport coupled proton transport / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding / aerobic respiration / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase, subunit 15 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily / Alpha-Beta Plaits - #3270 / NADH-quinone oxidoreductase subunit E / Rossmann fold - #12280 ...NADH-quinone oxidoreductase, subunit 15 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1450 / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Metal Transport, Frataxin; Chain A / Frataxin/CyaY superfamily / Alpha-Beta Plaits - #3270 / NADH-quinone oxidoreductase subunit E / Rossmann fold - #12280 / Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Ubiquitin-like (UB roll) - #600 / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / de novo design (two linked rop proteins) / Cro/C1-type helix-turn-helix domain / 2Fe-2S iron-sulfur cluster binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like 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:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / Aspartate decarboxylase-like domain superfamily / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / : / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / 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. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / 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 / 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) / Arc Repressor Mutant, subunit A / Thioredoxin-like superfamily / Alpha-Beta Plaits / Roll / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 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 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 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: 3.1 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_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_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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,51650
Polymers562,32316
Non-polymers8,19334
Water00
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)285,28226
Polymers281,1618
Non-polymers4,12118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39370 Å2
ΔGint-400 kcal/mol
Surface area81540 Å2
MethodPISA
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)285,23424
Polymers281,1618
Non-polymers4,07216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39170 Å2
ΔGint-379 kcal/mol
Surface area81560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.002, 151.015, 216.624
Angle α, β, γ (deg.)90.000, 93.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
113
21C
121
22A
134
23D
145
24E
152
25B
169
26G
176
27F
187
28H

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
112THRTHRARGARGchain 1 and (resseq 2:438 )1A2 - 4382 - 438
212THRTHRARGARGchain A and (resseq 2:438 )AI2 - 4382 - 438
113VALVALGLYGLYchain 4 and (resseq 25:31 or resseq 39:409 )4D25 - 3125 - 31
123GLYGLYARGARGchain 4 and (resseq 25:31 or resseq 39:409 )4D39 - 40939 - 409
213VALVALGLYGLYchain D and (resseq 25:31 or resseq 39:409 )DL25 - 3125 - 31
223GLYGLYARGARGchain D and (resseq 25:31 or resseq 39:409 )DL39 - 40939 - 409
114METMETTRPTRPchain 5 and (resseq 1:196 )5E1 - 1961 - 196
214METMETTRPTRPchain E and (resseq 1:196 )EM1 - 1961 - 196
115GLYGLYGLUGLUchain 2 and (resseq 2:180 )2B2 - 1802 - 180
215GLYGLYGLUGLUchain B and (resseq 2:180 )BJ2 - 1802 - 180
116TYRTYRGLYGLYchain 9 and (resseq 26:179 )9G26 - 17926 - 179
216TYRTYRGLYGLYchain G and (resseq 26:179 )GO26 - 17926 - 179
117GLUGLUALAALAchain 6 and (resseq 15:56 or resseq 74:175 )6F15 - 5615 - 56
127GLNGLNALAALAchain 6 and (resseq 15:56 or resseq 74:175 )6F74 - 17574 - 175
217GLUGLUALAALAchain F and (resseq 15:56 or resseq 74:175 )FN15 - 5615 - 56
227GLNGLNALAALAchain F and (resseq 15:56 or resseq 74:175 )FN74 - 17574 - 175
118ALAALAALAALAchain 7 and (resseq 3:129 )7H3 - 1293 - 129
218ALAALAALAALAchain H and (resseq 3:129 )HP3 - 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, 16 molecules 1A2B3C4D5E6F9G7H

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


Mass: 48693.715 Da / Num. of mol.: 2 / 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 I chain 2 / NDH-1 subunit 2


Mass: 20309.162 Da / Num. of mol.: 2 / 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 I chain 3 / NDH-1 subunit 3


Mass: 86656.203 Da / Num. of mol.: 2 / 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 I chain 4 / NDH-1 subunit 4


Mass: 46428.027 Da / Num. of mol.: 2 / 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 I chain 5 / NDH-1 subunit 5


Mass: 23893.254 Da / Num. of mol.: 2 / 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 I subunit 6 / NDH-1 subunit 6


Mass: 20262.564 Da / Num. of mol.: 2 / 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 I subunit 9 / NDH-1 subunit 9


Mass: 20106.309 Da / Num. of mol.: 2 / 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 I chain 15 / NDH-1 subunit 15


Mass: 14812.074 Da / Num. of mol.: 2 / 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 , 6 types, 34 molecules

#9: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#11: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#12: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#13: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#14: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.05 M NaCl, 0.1 M MgCl2, 7% PEG4000, 3 mM NADH, 5 mM sodium dithionite, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97654 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2007
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97654 Å / Relative weight: 1
ReflectionRedundancy: 2.5 % / Av σ(I) over netI: 3.2 / Number: 134538 / Rmerge(I) obs: 0.205 / Rsym value: 0.205 / D res high: 4 Å / D res low: 29.913 Å / Num. obs: 53359 / % possible obs: 90.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
12.65124.0478.910.0650.0652.8
8.9412.6587.210.070.072.7
7.38.9485.910.0970.0972.5
6.327.386.210.1630.1632.5
5.666.3289.310.2360.2362.5
5.165.6690.610.2780.2782.5
4.785.1691.510.3020.3022.5
4.474.7892.110.3550.3552.5
4.224.4792.710.4850.4852.5
44.229310.6650.6652.5
ReflectionResolution: 3.1→29.913 Å / Num. all: 111667 / Num. obs: 111667 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 62.81 Å2 / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/σ(I): 7.4
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.4 / Num. measured all: 43457 / Num. unique all: 16621 / Rsym value: 0.586 / % possible all: 90.2

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FUG

2fug


Resolution: 3.1→29.571 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.801 / SU ML: 0.55 / Isotropic thermal model: Isotropic restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 27.37 / Stereochemistry target values: MLHL
Details: Native structure factors and HL coefficients are from phasing run in SHARP on native and Fe-peak datasets
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2215 1.94 %RANDOM
Rwork0.231 ---
all0.232 114079 --
obs0.232 111667 89.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.845 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso max: 140.95 Å2 / Biso mean: 62.22 Å2 / Biso min: 0.71 Å2
Baniso -1Baniso -2Baniso -3
1--7.678 Å20 Å23.523 Å2
2---3.911 Å20 Å2
3---6.594 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37316 0 290 0 37606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00938688
X-RAY DIFFRACTIONf_angle_d1.37552756
X-RAY DIFFRACTIONf_chiral_restr0.0915672
X-RAY DIFFRACTIONf_plane_restr0.0066802
X-RAY DIFFRACTIONf_dihedral_angle_d21.41614442
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
1135881X-RAY DIFFRACTIONPOSITIONAL0.032
12C5881X-RAY DIFFRACTIONPOSITIONAL0.032
2113417X-RAY DIFFRACTIONPOSITIONAL0.036
22A3417X-RAY DIFFRACTIONPOSITIONAL0.036
3143018X-RAY DIFFRACTIONPOSITIONAL0.032
32D3018X-RAY DIFFRACTIONPOSITIONAL0.032
4151608X-RAY DIFFRACTIONPOSITIONAL0.032
42E1608X-RAY DIFFRACTIONPOSITIONAL0.032
5121411X-RAY DIFFRACTIONPOSITIONAL0.034
52B1411X-RAY DIFFRACTIONPOSITIONAL0.034
6191194X-RAY DIFFRACTIONPOSITIONAL0.037
62G1194X-RAY DIFFRACTIONPOSITIONAL0.037
7161103X-RAY DIFFRACTIONPOSITIONAL0.035
72F1103X-RAY DIFFRACTIONPOSITIONAL0.035
8171031X-RAY DIFFRACTIONPOSITIONAL0.032
82H1031X-RAY DIFFRACTIONPOSITIONAL0.032
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 (%)
3.1-3.2630.3973160.35715700160161570089
3.263-3.4670.3453200.31815859161791585990
3.467-3.7350.3093460.27715777161231577789
3.735-4.110.2673220.23515899162211589990
4.11-4.7020.2283040.216517168211651793
4.702-5.9170.2132960.18216268165641626891
5.917-29.5720.2013110.17615844161551584488

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • 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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