[English] 日本語
Yorodumi
- PDB-4z3x: Active site complex BamBC of Benzoyl Coenzyme A reductase in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z3x
TitleActive site complex BamBC of Benzoyl Coenzyme A reductase in complex with 1-Monoenoyl-CoA
Components
  • Benzoyl-CoA reductase, putative
  • Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
KeywordsOXIDOREDUCTASE / aromatics / reductase / Benzoyl-CoA / anaerobic
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
4Fe-4S binding domain / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2 / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2 / Aldehyde Ferredoxin Oxidoreductase; A, domain 1 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal ...4Fe-4S binding domain / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2 / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2 / Aldehyde Ferredoxin Oxidoreductase; A, domain 1 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, N-terminal domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,5 Dienoyl-CoA / Chem-MTE / TRIETHYLENE GLYCOL / IRON/SULFUR CLUSTER / Unknown ligand / : / Benzoyl-CoA reductase, putative / Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
Similarity search - Component
Biological speciesGeobacter metallireducens GS-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWeinert, T. / Kung, J.W. / Weidenweber, S. / Huwiler, S.G. / Boll, M. / Ermler, U.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Structural basis of enzymatic benzene ring reduction.
Authors: Weinert, T. / Huwiler, S.G. / Kung, J.W. / Weidenweber, S. / Hellwig, P. / Stark, H.J. / Biskup, T. / Weber, S. / Cotelesage, J.J. / George, G.N. / Ermler, U. / Boll, M.
History
DepositionApr 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jul 8, 2015Group: Database references
Revision 1.3Jul 29, 2015Group: Database references
Revision 1.4Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Benzoyl-CoA reductase, putative
B: Benzoyl-CoA reductase, putative
C: Benzoyl-CoA reductase, putative
D: Benzoyl-CoA reductase, putative
E: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
F: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
G: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
H: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,87952
Polymers376,1188
Non-polymers13,76144
Water20,7351151
1
A: Benzoyl-CoA reductase, putative
B: Benzoyl-CoA reductase, putative
E: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
F: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,91726
Polymers188,0594
Non-polymers6,85822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19580 Å2
ΔGint-302 kcal/mol
Surface area56950 Å2
MethodPISA
2
C: Benzoyl-CoA reductase, putative
D: Benzoyl-CoA reductase, putative
G: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
H: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,96126
Polymers188,0594
Non-polymers6,90322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19260 Å2
ΔGint-297 kcal/mol
Surface area55990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.767, 116.256, 143.973
Angle α, β, γ (deg.)90.00, 110.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:653 )
211chain 'B' and (resseq 1:653 )

-
Components

-
Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Benzoyl-CoA reductase, putative


Mass: 73895.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Gene: bamB-1, Gmet_2087 / Production host: Geobacter metallireducens GS-15 (bacteria) / References: UniProt: Q39TV8
#2: Protein
Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein


Mass: 20133.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Gene: bamC-1, Gmet_2086 / Production host: Geobacter metallireducens GS-15 (bacteria) / References: UniProt: Q39TV9

-
Non-polymers , 9 types, 1195 molecules

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


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#5: Chemical
ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: W
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-4KX / 1,5 Dienoyl-CoA / Cyclohex-1,5-diene-1-carbonyl-CoA


Mass: 873.656 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H42N7O17P3S
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG 4000, 0.2 M LiCl, 2 mM DTT, 0.2 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.25 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 1.85→88.071 Å / Num. all: 330481 / Num. obs: 306743 / % possible obs: 92.8 % / Redundancy: 2.6 % / Rsym value: 0.094 / Net I/σ(I): 5.46
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 1.7 % / Rmerge(I) obs: 1.384 / Mean I/σ(I) obs: 0.47 / % possible all: 66.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOR

1aor


Resolution: 1.85→88.071 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 4087 1.33 %
Rwork0.1856 --
obs0.1862 306311 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→88.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25821 0 599 1151 27571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0227288
X-RAY DIFFRACTIONf_angle_d1.67636937
X-RAY DIFFRACTIONf_dihedral_angle_d15.9910422
X-RAY DIFFRACTIONf_chiral_restr0.0833925
X-RAY DIFFRACTIONf_plane_restr0.0094791
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5171X-RAY DIFFRACTIONPOSITIONAL
12B5171X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8498-1.87160.5308590.52734050X-RAY DIFFRACTION36
1.8716-1.89440.44151220.46857060X-RAY DIFFRACTION63
1.8944-1.91840.46211010.44068136X-RAY DIFFRACTION73
1.9184-1.94360.47431210.39378769X-RAY DIFFRACTION78
1.9436-1.97020.36061230.3679516X-RAY DIFFRACTION85
1.9702-1.99840.35911350.34949981X-RAY DIFFRACTION89
1.9984-2.02820.34311460.339510643X-RAY DIFFRACTION95
2.0282-2.05990.32331370.31711051X-RAY DIFFRACTION98
2.0599-2.09370.33351400.296211073X-RAY DIFFRACTION99
2.0937-2.12980.34481540.280411166X-RAY DIFFRACTION99
2.1298-2.16850.30961590.264211139X-RAY DIFFRACTION99
2.1685-2.21020.31421900.250511035X-RAY DIFFRACTION99
2.2102-2.25530.32661310.23611207X-RAY DIFFRACTION99
2.2553-2.30440.261550.226811093X-RAY DIFFRACTION99
2.3044-2.3580.25871610.216111127X-RAY DIFFRACTION99
2.358-2.4170.29731420.208711187X-RAY DIFFRACTION99
2.417-2.48230.27981560.207811132X-RAY DIFFRACTION99
2.4823-2.55540.2471410.195711143X-RAY DIFFRACTION99
2.5554-2.63790.28171460.191911170X-RAY DIFFRACTION99
2.6379-2.73210.23221470.19311115X-RAY DIFFRACTION99
2.7321-2.84150.23961440.195211093X-RAY DIFFRACTION99
2.8415-2.97090.26571450.199911169X-RAY DIFFRACTION99
2.9709-3.12750.23391430.194111110X-RAY DIFFRACTION99
3.1275-3.32350.23141580.186411031X-RAY DIFFRACTION98
3.3235-3.58010.22831400.172210946X-RAY DIFFRACTION97
3.5801-3.94040.19561450.147810979X-RAY DIFFRACTION97
3.9404-4.51050.15771490.12611061X-RAY DIFFRACTION98
4.5105-5.68260.17421430.120310927X-RAY DIFFRACTION96
5.6826-88.17060.16651540.131211115X-RAY DIFFRACTION96
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)
11.33-0.2003-0.73890.96580.18730.8831-0.0735-0.2473-0.3394-0.1119-0.1399-0.21330.2080.1975-0.06670.41850.03890.09850.28540.11460.406155.777616.689317.5325
21.39980.0917-0.80150.91870.00851.19090.12660.04180.0993-0.2724-0.0463-0.0339-0.1991-0.0628-0.11780.41330.01960.0620.16910.02790.230841.56431.18739.2426
30.67920.1976-0.53810.66230.06040.47830.03070.50390.1696-1.11970.0869-0.5117-0.1085-0.2663-0.02570.99180.0330.07370.34170.02050.039742.972625.8204-13.9364
41.05010.0585-0.66860.6705-0.49250.76190.1802-0.21120.1313-0.2347-0.1332-0.3587-0.25590.2543-0.26490.5358-0.04870.18010.3062-0.00790.458463.837340.09947.1997
51.111-0.1423-0.49251.1575-0.65411.5447-0.0284-0.1656-0.175-0.3576-0.2012-0.51030.03540.4109-0.13590.49730.03820.24350.36130.08650.657875.549525.09222.7385
60.8681-0.00320.02550.2633-0.08420.60830.7302-0.10021.079-0.3936-0.2238-0.2347-0.7394-0.38560.10350.78990.18410.46760.26160.03010.9565-8.576156.809637.6276
70.3621-0.10620.30860.0302-0.12020.25130.45970.81570.4962-0.7026-0.13420.0288-0.2217-0.19590.04171.230.40550.25811.09190.42480.8132-6.704951.35925.8674
80.0020.04640.08690.0273-0.01270.01150.61350.65791.0089-0.4552-0.1174-0.0346-0.6783-0.21390.38511.57080.5970.78440.60120.84281.5221-5.2869.006814.6348
90.6810.0440.0610.3454-0.19650.21820.390.57360.6304-0.43540.04740.3795-0.4117-0.71950.20070.8030.40770.09120.94410.35160.863-29.531952.246921.2801
101.4407-0.0546-0.48180.92960.46571.11290.05650.1419-0.0347-0.2335-0.0376-0.3131-0.1357-0.0343-0.1520.22450.06780.01850.26090.05540.4223-29.456355.599769.5018
110.5095-0.1732-0.39530.10810.22050.4189-0.0673-0.3753-0.17660.4346-0.1321-0.20450.32430.0649-0.050.50670.0273-0.16880.58210.11710.5171-33.687445.8917100.0399
120.8943-0.4184-0.62030.75650.17170.67160.0452-0.32250.08190.16850.0363-0.4014-0.05210.1855-0.1720.25330.0224-0.18240.40060.00920.3907-31.773863.820994.413
130.567-0.4356-0.40920.4531-0.02861.2907-0.211-0.5317-0.28190.2860.153-0.23430.36990.3259-0.08540.32680.1153-0.20110.61670.10940.8678-15.127641.770393.6171
140.8089-0.2627-0.36720.68110.0960.529-0.0752-0.4037-0.32310.19860.1283-0.6020.07790.4623-0.02250.19160.1575-0.11690.50170.14330.9359-11.850744.072484.9253
150.5755-0.2876-0.31560.50310.34051.96850.2008-0.39070.1836-0.0430.3156-0.6881-0.29040.7088-0.07110.2003-0.0448-0.01430.72790.01791.14230.193756.183879.3677
160.51070.29730.12650.52270.26560.1743-0.3680.5162-0.6733-0.0623-0.08720.50280.5287-0.2792-0.32490.2946-0.3624-0.05940.4721-0.63890.7683-98.479820.318681.919
171.2773-0.0169-0.35560.51650.51990.9283-0.30720.4164-0.78030.058-0.05560.28140.3911-0.21630.05140.3309-0.03780.02510.3905-0.20310.5278-85.81423.72885.1823
181.0163-0.1693-0.71840.80070.00850.54030.145-0.17650.15430.447-0.03960.227-0.42260.2550.13330.4518-0.0937-0.01820.3893-0.08840.2363-81.602547.0428103.4741
191.4606-0.1623-0.55551.02840.06821.1296-0.3025-0.2651-0.65220.46930.00770.20450.30480.25860.28880.45220.0470.05550.35870.05940.3685-83.477128.9315108.9157
200.7293-0.1099-0.39371.3684-0.161.13-0.04510.386-0.25930.3017-0.07530.82610.0052-0.43450.3250.2725-0.0390.01380.5173-0.15010.5664-107.370239.692595.0586
211.6012-0.458-0.69241.05180.24681.14960.1713-0.36490.34860.103-0.09360.09-0.18230.0831-0.17790.3915-0.06840.09450.3162-0.04050.254735.971736.52333.2752
221.5206-0.0048-0.57480.75680.09090.97520.1595-0.1620.05110.0308-0.05540.1294-0.13290.0366-0.0820.4085-0.01950.06620.2873-0.00870.279824.91729.332933.7928
232.4285-0.87-1.22290.86160.62720.68560.2587-0.6810.4110.18290.0676-0.2-0.26340.6219-0.27940.6281-0.13120.09840.5008-0.13730.353741.175543.126138.6422
240.90610.23360.39320.97520.03950.25050.1386-0.59370.44790.14230.02850.1325-0.15580.199-0.23240.5526-0.12290.18880.4256-0.14730.521527.835748.221940.7066
252.6814-0.4248-1.47384.59070.39782.4090.0717-0.39820.0620.04670.11530.2279-0.02620.03230.00580.4786-0.02750.04410.7084-0.05280.55393.498232.890857.5292
261.221-0.6994-1.31641.95630.06881.7187-0.0731-0.3649-0.44540.08490.083-0.05360.38690.33820.01660.56420.0885-0.03240.81730.12930.53526.078221.388161.3182
271.5179-0.2459-0.96710.52470.28951.14270.25360.03160.1772-0.1567-0.10810.0746-0.169-0.098-0.05440.33990.02650.02010.29520.0390.27323.406433.371634.82
281.18940.0866-0.75660.3990.16330.83210.4271-0.12080.4946-0.157-0.0792-0.0051-0.43480.0586-0.15270.4241-0.04580.09720.2726-0.0690.347817.844940.195134.7571
291.5961-0.3485-0.76280.29380.4541.56880.326-0.35760.3384-0.2595-0.0878-0.0192-0.29210.1534-0.14560.3966-0.04310.04510.3564-0.05960.287313.129237.6241.8843
301.7919-0.0854-1.01290.21410.43021.2650.08320.0579-0.1514-0.2205-0.09420.08370.1608-0.19150.05730.41540.0154-0.0510.31440.03360.26763.418524.594129.6259
313.2543-2.527-3.42983.6374.39616.1088-0.08150.1187-0.2094-0.1494-0.2233-0.19760.16020.25740.04980.62090.07380.01460.67380.07560.517819.319615.990741.3273
322.8110.30950.23813.97881.66593.7641-0.0801-0.1065-0.1295-0.0134-0.0532-0.18190.30680.1717-0.07270.3828-0.0513-0.02690.7664-0.03790.393912.484129.060455.6273
332.2901-1.181-2.54042.84-0.21564.06960.0442-0.7043-0.14190.26440.26520.21590.17170.0905-0.02610.5001-0.0526-0.05071.0253-0.10630.41667.755129.940966.7492
341.3913-0.2822-0.61580.81870.1020.8455-0.03050.2764-0.3482-0.224-0.087-0.3260.0822-0.20310.10890.27640.01250.02530.3543-0.07710.4212-47.43235.475867.9517
351.2352-0.2816-0.67890.4450.18611.1890.11380.3697-0.0559-0.2952-0.1213-0.213-0.198-0.17080.05220.34550.0218-0.02660.5054-0.03660.3474-55.139441.163464.7236
362.9788-0.5507-1.37161.7434-0.13021.2289-0.00820.2662-0.3829-0.1268-0.117-0.0420.33280.07240.16660.39780.01070.08150.4067-0.07460.7348-40.774224.691368.8414
374.24730.9354-0.36581.4143-0.01531.3779-0.24160.1514-0.50970.0639-0.0216-0.04440.2985-0.04140.19660.35780.01310.02540.31860.0040.5679-49.781123.326775.7718
383.11810.1744-1.41171.5722-0.34992.6968-0.02190.3785-0.4215-0.11020.01540.24010.1365-0.64740.2520.8251-0.1527-0.00421.2305-0.18380.7969-61.303919.509558.9394
393.99150.1064-0.34595.5892-0.35154.6443-0.06740.7009-0.1774-0.3356-0.24880.1374-0.0465-0.37060.16050.5137-0.0504-0.01140.985-0.17090.5723-52.554333.807947.061
400.28140.4099-0.31540.7859-0.00391.43230.19780.99670.1001-0.3197-0.29340.2065-0.3212-0.68010.08641.1807-0.2873-0.04691.65650.05560.5552-48.059136.210436.3013
411.1153-0.23430.31081.2131-0.15350.18140.0440.53460.1327-0.3147-0.16540.08740.0144-0.1360.0090.2743-0.0122-0.10580.6577-0.12890.1799-73.272644.54869.8593
420.1289-0.14830.23390.2058-0.29880.448-0.0360.3368-0.1127-0.2480.00320.12090.0437-0.11140.02460.3102-0.031-0.28120.9872-0.44420.362-87.461436.170862.7517
430.6873-0.3081-0.32780.5508-0.30910.7067-0.10110.3459-0.2628-0.0132-0.1380.148-0.0051-0.342-0.20490.0846-0.0454-0.23720.5509-0.24430.1152-72.221234.949175.5256
441.7461-0.2546-0.49311.0029-0.00380.3205-0.02320.5591-0.5157-0.2201-0.20850.01420.2107-0.29610.19010.2943-0.03310.0040.478-0.15790.4177-63.006430.389468.6423
451.40340.1695-0.09582.76061.60761.6083-0.05120.6859-0.247-0.2383-0.10650.10240.1309-0.21790.20270.4552-0.0818-0.08420.8361-0.23250.3682-75.308732.022859.4956
460.95540.1143-0.76340.3831-0.2270.89030.22170.75570.1804-0.2866-0.18310.0911-0.2853-0.42740.02950.41080.1054-0.07380.6927-0.03060.3144-80.293847.717365.2059
472.5993-1.061-1.77630.80650.81981.21220.17230.7360.2962-0.1913-0.0939-0.3016-0.3018-0.2337-0.04540.25090.0447-0.12340.73650.03190.3533-66.49951.283464.9016
484.8666-0.4698-0.37241.68842.35693.430.12990.5629-0.2341-0.3075-0.0482-0.1380.0009-0.20970.12180.7483-0.01050.17080.9237-0.23770.7245-42.122834.339946.5872
490.9427-0.4028-1.06590.37890.42041.2252-0.0050.8236-0.1846-0.2604-0.09690.2243-0.0008-0.55550.22121.0048-0.28350.2611.4061-0.44410.9207-47.305426.306440.4059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 349 )
3X-RAY DIFFRACTION3chain 'A' and (resid 350 through 433 )
4X-RAY DIFFRACTION4chain 'A' and (resid 434 through 604 )
5X-RAY DIFFRACTION5chain 'A' and (resid 605 through 653 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 232 )
7X-RAY DIFFRACTION7chain 'B' and (resid 233 through 297 )
8X-RAY DIFFRACTION8chain 'B' and (resid 298 through 433 )
9X-RAY DIFFRACTION9chain 'B' and (resid 434 through 653 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 232 )
11X-RAY DIFFRACTION11chain 'C' and (resid 233 through 297 )
12X-RAY DIFFRACTION12chain 'C' and (resid 298 through 442 )
13X-RAY DIFFRACTION13chain 'C' and (resid 443 through 481 )
14X-RAY DIFFRACTION14chain 'C' and (resid 482 through 604 )
15X-RAY DIFFRACTION15chain 'C' and (resid 605 through 653 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 77 )
17X-RAY DIFFRACTION17chain 'D' and (resid 78 through 232 )
18X-RAY DIFFRACTION18chain 'D' and (resid 233 through 297 )
19X-RAY DIFFRACTION19chain 'D' and (resid 298 through 442 )
20X-RAY DIFFRACTION20chain 'D' and (resid 443 through 652 )
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 57 )
22X-RAY DIFFRACTION22chain 'E' and (resid 58 through 114 )
23X-RAY DIFFRACTION23chain 'E' and (resid 115 through 127 )
24X-RAY DIFFRACTION24chain 'E' and (resid 128 through 148 )
25X-RAY DIFFRACTION25chain 'E' and (resid 149 through 163 )
26X-RAY DIFFRACTION26chain 'E' and (resid 164 through 174 )
27X-RAY DIFFRACTION27chain 'F' and (resid 7 through 54 )
28X-RAY DIFFRACTION28chain 'F' and (resid 55 through 84 )
29X-RAY DIFFRACTION29chain 'F' and (resid 85 through 114 )
30X-RAY DIFFRACTION30chain 'F' and (resid 115 through 140 )
31X-RAY DIFFRACTION31chain 'F' and (resid 141 through 150 )
32X-RAY DIFFRACTION32chain 'F' and (resid 151 through 163 )
33X-RAY DIFFRACTION33chain 'F' and (resid 164 through 176 )
34X-RAY DIFFRACTION34chain 'G' and (resid 7 through 74 )
35X-RAY DIFFRACTION35chain 'G' and (resid 75 through 114 )
36X-RAY DIFFRACTION36chain 'G' and (resid 115 through 127 )
37X-RAY DIFFRACTION37chain 'G' and (resid 128 through 140 )
38X-RAY DIFFRACTION38chain 'G' and (resid 141 through 150 )
39X-RAY DIFFRACTION39chain 'G' and (resid 151 through 163 )
40X-RAY DIFFRACTION40chain 'G' and (resid 164 through 175 )
41X-RAY DIFFRACTION41chain 'H' and (resid 6 through 33 )
42X-RAY DIFFRACTION42chain 'H' and (resid 34 through 43 )
43X-RAY DIFFRACTION43chain 'H' and (resid 44 through 64 )
44X-RAY DIFFRACTION44chain 'H' and (resid 65 through 104 )
45X-RAY DIFFRACTION45chain 'H' and (resid 105 through 114 )
46X-RAY DIFFRACTION46chain 'H' and (resid 115 through 127 )
47X-RAY DIFFRACTION47chain 'H' and (resid 128 through 151 )
48X-RAY DIFFRACTION48chain 'H' and (resid 152 through 163 )
49X-RAY DIFFRACTION49chain 'H' and (resid 164 through 174 )

+
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