[English] 日本語
Yorodumi
- PDB-4gd3: Structure of E. coli hydrogenase-1 in complex with cytochrome b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gd3
TitleStructure of E. coli hydrogenase-1 in complex with cytochrome b
Components
  • (Hydrogenase-1 ...) x 2
  • Ni/Fe-hydrogenase 1 B-type cytochrome subunit
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / O2-tolerant H2:quinone oxidoreductase / membrane-bound / Ni-Fe-hydrogenase-cytochrome B complex / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / cellular response to starvation / 4 iron, 4 sulfur cluster binding / outer membrane-bounded periplasmic space / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Nickel-dependent hydrogenase b-type cytochrome subunit / Nickel-dependent hydrogenases b-type cytochrome subunit signature 1. / Nickel-dependent hydrogenases b-type cytochrome subunit signature 2. / Cytochrome b561, bacterial/Ni-hydrogenase / Prokaryotic cytochrome b561 / Fumarate Reductase Cytochrome B subunit / Transmembrane di-heme cytochromes, Chain C / Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit ...Nickel-dependent hydrogenase b-type cytochrome subunit / Nickel-dependent hydrogenases b-type cytochrome subunit signature 1. / Nickel-dependent hydrogenases b-type cytochrome subunit signature 2. / Cytochrome b561, bacterial/Ni-hydrogenase / Prokaryotic cytochrome b561 / Fumarate Reductase Cytochrome B subunit / Transmembrane di-heme cytochromes, Chain C / Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Di-haem cytochrome, transmembrane / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE4-S3 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / IRON/SULFUR CLUSTER / Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit / Hydrogenase-1 large chain / Hydrogenase-1 small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C. / Darnault, C.
Citation
Journal: Structure / Year: 2013
Title: Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b.
Authors: Volbeda, A. / Darnault, C. / Parkin, A. / Sargent, F. / Armstrong, F.A. / Fontecilla-Camps, J.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.
Authors: Volbeda, A. / Amara, P. / Darnault, C. / Mouesca, J.M. / Parkin, A. / Roessler, M.M. / Armstrong, F.A. / Fontecilla-Camps, J.C.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: Hydrogenase-1 small chain
L: Hydrogenase-1 large chain
T: Hydrogenase-1 small chain
M: Hydrogenase-1 large chain
Q: Hydrogenase-1 small chain
J: Hydrogenase-1 large chain
R: Hydrogenase-1 small chain
K: Hydrogenase-1 large chain
A: Ni/Fe-hydrogenase 1 B-type cytochrome subunit
B: Ni/Fe-hydrogenase 1 B-type cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,13850
Polymers461,54110
Non-polymers8,59740
Water72140
1
S: Hydrogenase-1 small chain
L: Hydrogenase-1 large chain
T: Hydrogenase-1 small chain
M: Hydrogenase-1 large chain
A: Ni/Fe-hydrogenase 1 B-type cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,06925
Polymers230,7705
Non-polymers4,29820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32640 Å2
ΔGint-358 kcal/mol
Surface area59610 Å2
MethodPISA
2
S: Hydrogenase-1 small chain
L: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,92011
Polymers101,5722
Non-polymers1,3489
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-114 kcal/mol
Surface area29120 Å2
MethodPISA
3
T: Hydrogenase-1 small chain
M: Hydrogenase-1 large chain
A: Ni/Fe-hydrogenase 1 B-type cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,14914
Polymers129,1983
Non-polymers2,95011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15340 Å2
ΔGint-183 kcal/mol
Surface area38310 Å2
MethodPISA
4
Q: Hydrogenase-1 small chain
J: Hydrogenase-1 large chain
R: Hydrogenase-1 small chain
K: Hydrogenase-1 large chain
B: Ni/Fe-hydrogenase 1 B-type cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,06925
Polymers230,7705
Non-polymers4,29820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32600 Å2
ΔGint-356 kcal/mol
Surface area59690 Å2
MethodPISA
5
Q: Hydrogenase-1 small chain
J: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,92011
Polymers101,5722
Non-polymers1,3489
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-114 kcal/mol
Surface area29180 Å2
MethodPISA
6
R: Hydrogenase-1 small chain
K: Hydrogenase-1 large chain
B: Ni/Fe-hydrogenase 1 B-type cytochrome subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,14914
Polymers129,1983
Non-polymers2,95011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-181 kcal/mol
Surface area38380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.000, 165.300, 212.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11S
21T
12S
22Q
13S
23Q
14L
24M
15L
25J
16Q
26R
17T
27R
18T
28R
19M
29K
110J
210K
111A
211B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111S4 - 21
2111T4 - 21
1211S23 - 60
2211T23 - 60
1311S62 - 97
2311T62 - 97
1411S99 - 100
2411T99 - 100
1511S102 - 109
2511T102 - 109
1611S111 - 121
2611T111 - 121
1711S128 - 135
2711T128 - 135
1811S137 - 152
2811T137 - 152
1911S155 - 167
2911T155 - 167
11011S169 - 170
21011T169 - 170
11111S176 - 184
21111T176 - 184
11211S186 - 187
21211T186 - 187
11311S189 - 195
21311T189 - 195
11411S200 - 202
21411T200 - 202
11511S204 - 210
21511T204 - 210
11611S212 - 216
21611T212 - 216
11711S219 - 221
21711T219 - 221
11811S223 - 226
21811T223 - 226
11911S228 - 233
21911T228 - 233
12011S235 - 259
22011T235 - 259
12111S261 - 263
22111T261 - 263
12211S341 - 403
22211T341 - 403
1121S4 - 264
2121Q4 - 264
1221S341 - 505
2221Q341 - 405
1131S265 - 307
2131Q265 - 307
1141L2 - 60
2141M2 - 60
1241L65 - 96
2241M65 - 96
1341L99 - 233
2341M99 - 233
1441L235 - 243
2441M235 - 243
1541L246 - 247
2541M246 - 247
1641L249 - 255
2641M249 - 255
1741L257 - 486
2741M257 - 486
1841L490 - 522
2841M490 - 522
1941L524 - 582
2941M524 - 582
11041L583 - 603
21041M583 - 604
1151L2 - 582
2151J2 - 582
1251L583 - 603
2251J583 - 603
1351L591 - 604
2351J591 - 604
1161Q4 - 21
2161R4 - 21
1261Q23 - 60
2261R23 - 60
1361Q62 - 97
2361R62 - 97
1461Q99 - 100
2461R99 - 100
1561Q102 - 109
2561R102 - 109
1661Q111 - 121
2661R111 - 121
1761Q128 - 135
2761R128 - 135
1861Q137 - 152
2861R137 - 152
1961Q155 - 167
2961R155 - 167
11061Q169 - 170
21061R169 - 170
11161Q176 - 184
21161R176 - 184
11261Q186 - 187
21261R186 - 187
11361Q189 - 195
21361R189 - 195
11461Q200 - 202
21461R200 - 202
11561Q204 - 210
21561R204 - 210
11661Q212 - 216
21661R212 - 216
11761Q219 - 221
21761R219 - 221
11861Q223 - 226
21861R223 - 226
11961Q228 - 233
21961R228 - 233
12061Q235 - 259
22061R235 - 259
12161Q261 - 263
22161R261 - 263
12261Q341 - 403
22261R341 - 403
1171T4 - 264
2171R4 - 264
1271T341 - 403
2271R341 - 403
1371M351 - 601
2371K351 - 601
1181T265 - 303
2181R265 - 303
1191M2 - 582
2191K2 - 582
1291M583 - 604
2291K583 - 604
1391M591 - 605
2391K591 - 605
11101J2 - 60
21101K2 - 60
12101J65 - 96
22101K65 - 96
13101J99 - 233
23101K99 - 233
14101J235 - 243
24101K235 - 243
15101J246 - 247
25101K246 - 247
16101J249 - 255
26101K249 - 255
17101J257 - 486
27101K257 - 486
18101J490 - 522
28101K490 - 522
19101J524 - 582
29101K524 - 582
110101J583 - 603
210101K583 - 604
11111A8 - 89
21111B8 - 89
12111A103 - 115
22111B103 - 115
13111A127 - 210
23111B127 - 210
14111A301
24111B301
15111A302 - 314
25111B302 - 314

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

-
Components

-
Hydrogenase-1 ... , 2 types, 8 molecules STQRLMJK

#1: Protein
Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 36820.703 Da / Num. of mol.: 4 / Mutation: P287C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0972, hyaA, JW0954 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P69739, hydrogenase (acceptor)
#2: Protein
Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64751.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0973, hyaB, JW0955 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P0ACD8, hydrogenase (acceptor)

-
Protein / Sugars , 2 types, 6 molecules AB

#10: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Protein Ni/Fe-hydrogenase 1 B-type cytochrome subunit


Mass: 27626.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0974, hyaC, JW0956 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P0AAM1

-
Non-polymers , 8 types, 76 molecules

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


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-F4S / FE4-S3 CLUSTER / T-CLUSTER


Mass: 319.575 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3FeN2O
#8: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.9
Details: 12% PEG4000, 0.1M NaCl, 0.1M NaAc, 0.2M NH4Ac, 0.001M DTT, 0.02% DDM, Tris/HCl, 0.0003M NQNO (a menaquinone analog), pH 5.9, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 3.2→49.12 Å / Num. all: 73321 / Num. obs: 138472 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 89.561 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.35
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 1.054 / Mean I/σ(I) obs: 1.16 / Num. measured obs: 31713 / Num. unique obs: 12080 / % possible all: 97.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UQY

3uqy


Resolution: 3.3→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2157 / WRfactor Rwork: 0.1764 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8281 / SU B: 69.799 / SU ML: 0.487 / SU Rfree: 0.562
Isotropic thermal model: TLS + isotropic (possible thanks to tight ncs restraints)
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.562 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : RESIDUAL ONLY ANISOTROPIC B FACTORS ARE GENERATED FROM THE REFINED TLS PARAMETERS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3298 4.9 %RANDOM
Rwork0.1999 66534 --
all0.2018 67491 --
obs0.2018 66832 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.32 Å2 / Biso mean: 105.957 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-7.45 Å2-0 Å2-0 Å2
2---6.89 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 3.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30002 0 316 40 30358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02232380
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.95844196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2854168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94923.7931450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.099155048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.38515202
X-RAY DIFFRACTIONr_chiral_restr0.0820.24832
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02124938
X-RAY DIFFRACTIONr_mcbond_it0.8371.519834
X-RAY DIFFRACTIONr_mcangle_it1.6612.532034
X-RAY DIFFRACTIONr_scbond_it2.306312546
X-RAY DIFFRACTIONr_scangle_it3.834511924
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1S1728TIGHT POSITIONAL0.040.05
1S1728TIGHT THERMAL0.241
2S2080TIGHT POSITIONAL0.030.05
2S2080TIGHT THERMAL0.241
3S279TIGHT POSITIONAL0.030.05
3S279TIGHT THERMAL0.161
4L4599TIGHT POSITIONAL0.030.05
4L4599TIGHT THERMAL0.181
5L4747TIGHT POSITIONAL0.030.05
5L4747TIGHT THERMAL0.181
6Q1728TIGHT POSITIONAL0.040.05
6Q1728TIGHT THERMAL0.261
7T2054TIGHT POSITIONAL0.030.05
7T2054TIGHT THERMAL0.241
8T255TIGHT POSITIONAL0.030.05
8T255TIGHT THERMAL0.171
9M4762TIGHT POSITIONAL0.030.05
9M4762TIGHT THERMAL0.181
10J4599TIGHT POSITIONAL0.030.05
10J4599TIGHT THERMAL0.191
11A1485TIGHT POSITIONAL0.030.05
11A1485TIGHT THERMAL0.161
LS refinement shellResolution: 3.3→3.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 229 -
Rwork0.344 4592 -
all-4821 -
obs-4592 99.24 %
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)
10.76110.13630.31722.177-0.16212.3323-0.01280.0715-0.01830.28790.0833-0.0061-0.64530.0003-0.07060.61390.1040.28870.3470.01180.3882-3.674423.8229-24.9881
20.7615-0.2043-0.06721.66440.38521.6363-0.0448-0.10780.09570.9017-0.01650.2329-0.8145-0.27620.06131.26810.20160.32690.4794-0.01590.456-15.046635.5136-5.3414
31.3321-0.421-0.0882.4174-0.51162.07550.01130.1471-0.2836-0.16060.08221.06750.1428-0.7704-0.09360.1995-0.00610.2130.7312-0.02510.9546-30.0247-4.0693-33.4953
40.7673-0.0154-0.09392.6442-0.25051.7552-0.0584-0.048-0.49150.59340.01050.74140.4642-0.44850.04780.4339-0.06550.43480.55370.06630.9304-21.681-19.0479-14.9375
52.00190.3430.90961.72090.05282.39880.03950.7163-0.0044-1.0525-0.01570.7747-0.109-0.5005-0.02391.09470.1003-0.13350.9872-0.07090.7828-23.51854.2815-64.1598
61.0506-0.17940.59232.7236-0.57792.32060.02230.0973-0.2643-0.02370.1064-0.13250.14190.0787-0.12870.10480.05410.20610.429-0.04280.580522.3385-13.6936-35.8668
70.9864-0.22680.29782.1208-0.42941.30130.13340.1769-0.41690.29340.03-0.60880.25060.4926-0.16330.30.12940.07420.6436-0.11780.905144.5328-25.0916-30.1329
81.09520.39720.09131.42420.20911.5417-0.08190.49390.0239-0.27530.2181-0.1689-0.5710.3862-0.13630.697-0.11420.35780.74710.01290.460734.840814.501-60.1621
91.05270.05920.25221.5544-0.07810.8393-0.10110.2180.16840.20440.1226-0.3095-0.64520.439-0.02160.8534-0.26350.18230.6793-0.00240.579341.809729.4662-41.006
102.33960.3222-0.49422.4424-0.27482.21480.01920.9927-0.0455-1.3280.09380.3224-0.3533-0.1571-0.1131.36370.09780.13391.0106-0.02230.51778.38525.7913-77.3947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1S4 - 264
2X-RAY DIFFRACTION1S265 - 307
3X-RAY DIFFRACTION1S401 - 405
4X-RAY DIFFRACTION1S501 - 505
5X-RAY DIFFRACTION1T501 - 502
6X-RAY DIFFRACTION1Q501 - 505
7X-RAY DIFFRACTION1R501 - 502
8X-RAY DIFFRACTION2L2 - 582
9X-RAY DIFFRACTION2L601 - 604
10X-RAY DIFFRACTION2L701 - 703
11X-RAY DIFFRACTION3T4 - 264
12X-RAY DIFFRACTION3T265 - 303
13X-RAY DIFFRACTION3T401 - 403
14X-RAY DIFFRACTION3M601
15X-RAY DIFFRACTION4M2 - 582
16X-RAY DIFFRACTION4M602 - 605
17X-RAY DIFFRACTION4M701 - 703
18X-RAY DIFFRACTION5A8 - 89
19X-RAY DIFFRACTION5A103 - 115
20X-RAY DIFFRACTION5A127 - 210
21X-RAY DIFFRACTION5A301
22X-RAY DIFFRACTION5A302
23X-RAY DIFFRACTION5T404
24X-RAY DIFFRACTION6Q4 - 264
25X-RAY DIFFRACTION6Q265 - 307
26X-RAY DIFFRACTION6Q401 - 405
27X-RAY DIFFRACTION7J2 - 582
28X-RAY DIFFRACTION7J601 - 604
29X-RAY DIFFRACTION7J701 - 703
30X-RAY DIFFRACTION8R4 - 264
31X-RAY DIFFRACTION8R265 - 303
32X-RAY DIFFRACTION8R401 - 403
33X-RAY DIFFRACTION8K601
34X-RAY DIFFRACTION9K2 - 582
35X-RAY DIFFRACTION9K602 - 605
36X-RAY DIFFRACTION9K701 - 703
37X-RAY DIFFRACTION10B8 - 89
38X-RAY DIFFRACTION10B103 - 115
39X-RAY DIFFRACTION10B127 - 210
40X-RAY DIFFRACTION10B301
41X-RAY DIFFRACTION10B302
42X-RAY DIFFRACTION10R404

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more