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- PDB-4z40: Active site complex BamBC of Benzoyl Coenzyme A reductase as isolated -

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Basic information

Entry
Database: PDB / ID: 4z40
TitleActive site complex BamBC of Benzoyl Coenzyme A reductase as isolated
Components
  • Benzoyl-CoA reductase, putative
  • Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein
KeywordsOXIDOREDUCTASE / aromatics / 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
Chem-MTE / IRON/SULFUR CLUSTER / : / 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 / SAD / Resolution: 2.35 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 / struct_conn
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
Revision 2.0Oct 1, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.id / _chem_comp.name / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)386,00148
Polymers376,1188
Non-polymers9,88340
Water2,504139
1
A: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,00024
Polymers188,0594
Non-polymers4,94220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Benzoyl-CoA reductase, putative
C: 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)193,00024
Polymers188,0594
Non-polymers4,94220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.190, 116.820, 143.600
Angle α, β, γ (deg.)90.00, 110.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 1:652 )
211chain 'B' and (resseq 1:652 )
311chain 'C' and (resseq 1:652 )
411chain 'D' and (resseq 1:652 )

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Components

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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 (bacteria) / Strain (production host): GS-15 / 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 (bacteria) / Strain (production host): GS-15 / References: UniProt: Q39TV9

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Non-polymers , 7 types, 179 molecules

#3: Chemical
ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4
#5: 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
#6: Chemical
ChemComp-W / TUNGSTEN ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG 4000, 0.2 M LiCl, 2 mM DTT, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.214 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214 Å / Relative weight: 1
ReflectionResolution: 2.35→49.502 Å / Num. all: 161382 / Num. obs: 159502 / % possible obs: 98.8 % / Redundancy: 4.66 % / Rsym value: 0.17 / Net I/σ(I): 5.6
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 0.84 / % possible all: 99.1

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Processing

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

1aor


Resolution: 2.35→49.502 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1593 1 %
Rwork0.2123 --
obs0.2125 158727 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→49.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25818 0 336 139 26293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126955
X-RAY DIFFRACTIONf_angle_d0.95836449
X-RAY DIFFRACTIONf_dihedral_angle_d14.30110163
X-RAY DIFFRACTIONf_chiral_restr0.0383891
X-RAY DIFFRACTIONf_plane_restr0.0044688
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5180X-RAY DIFFRACTIONPOSITIONAL
12B5180X-RAY DIFFRACTIONPOSITIONAL0.022
13C5180X-RAY DIFFRACTIONPOSITIONAL0.022
14D5180X-RAY DIFFRACTIONPOSITIONAL0.023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.42590.43251430.416214234X-RAY DIFFRACTION99
2.4259-2.51260.41470.380314276X-RAY DIFFRACTION99
2.5126-2.61310.37951400.350614209X-RAY DIFFRACTION98
2.6131-2.73210.36491450.327114288X-RAY DIFFRACTION99
2.7321-2.87610.30111490.29514349X-RAY DIFFRACTION99
2.8761-3.05630.31721450.271214316X-RAY DIFFRACTION99
3.0563-3.29220.30421450.260514269X-RAY DIFFRACTION99
3.2922-3.62340.2451420.229514289X-RAY DIFFRACTION99
3.6234-4.14750.23391460.194414229X-RAY DIFFRACTION98
4.1475-5.22450.17411440.163314330X-RAY DIFFRACTION98
5.2245-49.51260.17641470.150814345X-RAY DIFFRACTION97
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)
10.50950.1760.24460.2430.13130.46591.1423-0.09891.395-0.3481-0.2843-0.4072-1.2633-0.3759-0.14971.65830.30051.07220.65930.09491.8083-8.511857.86637.2375
20.05320.2271-0.15780.6684-0.49290.37740.69380.98651.1665-1.162-0.28310.0155-0.8602-0.378-0.29462.12220.72160.67011.60850.59861.4861-4.541452.47388.553
30.326-0.1534-0.23970.2668-0.07420.35290.81811.39261.0919-1.1971-0.2909-0.0152-1.5588-1.1808-0.3732.52171.27020.83651.66770.95171.8-16.310361.975313.2567
40.47290.00390.25080.3142-0.18440.15860.80550.45580.7662-0.4334-0.18030.6117-0.8165-1.10330.18881.58911.08170.60141.620.51941.6257-30.535857.285227.3106
52.094-0.4923-0.58411.84680.85151.790.04740.1602-0.0281-0.41120.0526-0.5958-0.24970.0803-0.09340.51350.04320.24880.51360.03060.9347-29.377756.614569.4907
60.7248-0.8263-0.39444.3380.50260.86870.0585-0.5641-0.1151.154-0.194-1.03550.21630.17280.15450.85760.0596-0.14031.02310.10951.1549-28.859547.3341100.7932
70.7152-0.2381-0.10561.78230.67321.165-0.0381-0.2161-0.21710.03130.1377-0.89410.12540.4068-0.07050.43230.03580.02220.68560.04621.1378-19.739554.154289.2895
82.24450.1303-0.71231.8296-0.24362.2963-0.34970.6142-0.72780.0211-0.10890.30370.6285-0.38110.37140.6334-0.1650.26050.8247-0.31981.0586-89.466223.542784.1844
92.48460.6639-1.08160.7519-1.38684.53490.0392-0.2999-0.03050.3612-0.07320.1745-0.48430.28430.01550.589-0.05370.11570.6888-0.11790.726-79.470942.3295101.916
102.73-0.4551-1.11161.8425-0.49082.6626-0.1280.1307-0.30250.46510.04710.5763-0.0593-0.32920.07660.5447-0.09340.20850.7053-0.11780.8594-96.311438.6582102.0636
111.23560.97260.65671.57090.08340.7671-0.14790.3821-0.51830.4348-0.13130.81220.5431-1.10870.21140.7121-0.25020.35881.2882-0.29311.4856-112.575830.584998.2363
122.2410.4351-0.70431.6884-0.13461.9150.1266-0.4799-0.1461-0.1521-0.1042-0.2529-0.00580.4145-0.00930.6192-0.01210.28120.61780.00350.778847.413623.806515.5536
131.6509-0.3924-0.35821.27780.76344.15020.32690.22550.3815-0.3676-0.0696-0.0145-0.8977-0.1595-0.29370.910.06050.38920.57150.04041.015837.392742.09090.0956
142.28640.4887-0.54820.8609-0.26071.29620.2097-0.30670.0821-0.215-0.0984-0.3693-0.16610.4816-0.0930.8312-0.03840.39510.6603-0.02810.939360.023834.67211.04
152.0341-1.0453-0.40151.85920.4481.15240.3741-0.61250.48120.143-0.1738-0.0925-0.57130.3682-0.2320.8841-0.26430.42571.0373-0.21720.939437.078239.644935.6841
163.26950.6845-1.05411.9628-0.14931.34160.5131-0.46180.3030.0609-0.16370.0907-0.62020.2425-0.32480.7164-0.08020.30660.6383-0.07910.787925.326131.011631.0524
171.88742.6464-0.03626.2567-1.76841.16850.7178-0.39350.20660.6104-0.50430.1727-0.35770.0105-0.20930.8223-0.25370.24971.2422-0.11070.90334.472428.169342.2645
182.7024-0.5485-0.98281.17930.12071.5590.4203-0.84690.86520.28570.1401-0.1528-0.85131.0298-0.52191.2229-0.45350.46271.0336-0.38351.17536.937946.593637.402
192.2842-1.4753-1.78663.3504-2.68757.75720.5549-0.1508-0.10870.51790.21510.4564-1.28850.1702-0.691.2281-0.13130.11521.5613-0.03631.14965.784336.451357.0487
201.49520.1192-1.86330.6851-0.35012.38060.19990.0295-0.02990.130.1104-0.11130.055-0.1892-0.21361.29870.11230.21311.43960.0071.12995.683222.335561.1812
213.34010.3346-1.07220.7921-0.36851.82910.7216-0.28090.7051-0.303-0.0376-0.4635-0.65820.3628-0.57220.66680.00230.30030.5044-0.04630.73928.948335.384335.2749
222.301-0.8354-0.00743.81992.16495.50860.2454-0.66310.33660.1121-0.1214-0.37460.15290.9951-0.10320.9303-0.08740.121.5414-0.08611.101712.782926.215654.4924
232.61050.7299-0.50152.3941-0.23942.0754-0.2280.3456-0.4886-0.3773-0.0329-0.33360.2693-0.11430.26530.4550.00390.16450.4737-0.03730.9015-43.247632.455268.6788
243.8650.0379-0.84541.8663-0.29522.72640.00350.5701-0.2849-0.2919-0.1249-0.20560.1835-0.26320.12530.48640.00140.15670.5948-0.0610.6912-51.331137.590467.3219
258.1813-0.6272-0.47715.23441.01784.09130.7418-0.1501-0.2014-0.3436-0.11820.3472-0.4226-0.0259-0.59180.8557-0.05780.14651.323-0.32320.996-61.121420.567459.1283
260.70631.40190.30098.7709-4.11046.4038-0.1180.2081-0.4211-0.075-0.17490.51010.0703-0.07370.25750.7689-0.07640.16871.4635-0.22310.9336-52.471334.829346.9958
272.0135-0.4813-2.93772.54231.45944.51950.25590.8525-0.0549-0.5399-0.24410.1914-0.3433-0.4873-0.03172.3271-0.82140.25391.7004-0.27440.8177-48.160237.144836.0928
283.6509-0.3276-0.62892.6048-0.00521.6802-0.13660.5011-0.4615-0.303-0.0317-0.15310.1632-0.48980.15840.4574-0.10860.11390.8013-0.14640.616-70.068337.651270.6187
293.3282-1.0098-0.79992.07530.49462.71710.10870.93790.0192-0.4083-0.1722-0.0032-0.111-0.63770.02390.5559-0.04950.13650.9472-0.15070.6953-73.254142.232764.0792
304.25280.41630.70083.14710.15214.3062-0.23821.173-0.7413-1.3582-0.0069-0.81240.65670.65450.17711.3147-0.08090.47591.1845-0.24770.9477-44.057433.102744.2972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 233 )
2X-RAY DIFFRACTION2chain 'A' and (resid 234 through 317 )
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 531 )
4X-RAY DIFFRACTION4chain 'A' and (resid 532 through 652 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 233 )
6X-RAY DIFFRACTION6chain 'B' and (resid 234 through 278 )
7X-RAY DIFFRACTION7chain 'B' and (resid 279 through 652 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 233 )
9X-RAY DIFFRACTION9chain 'C' and (resid 234 through 354 )
10X-RAY DIFFRACTION10chain 'C' and (resid 355 through 564 )
11X-RAY DIFFRACTION11chain 'C' and (resid 565 through 652 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 257 )
13X-RAY DIFFRACTION13chain 'D' and (resid 258 through 349 )
14X-RAY DIFFRACTION14chain 'D' and (resid 350 through 652 )
15X-RAY DIFFRACTION15chain 'E' and (resid 6 through 43 )
16X-RAY DIFFRACTION16chain 'E' and (resid 44 through 104 )
17X-RAY DIFFRACTION17chain 'E' and (resid 105 through 114 )
18X-RAY DIFFRACTION18chain 'E' and (resid 115 through 140 )
19X-RAY DIFFRACTION19chain 'E' and (resid 141 through 163 )
20X-RAY DIFFRACTION20chain 'E' and (resid 164 through 174 )
21X-RAY DIFFRACTION21chain 'F' and (resid 7 through 140 )
22X-RAY DIFFRACTION22chain 'F' and (resid 141 through 176 )
23X-RAY DIFFRACTION23chain 'G' and (resid 7 through 43 )
24X-RAY DIFFRACTION24chain 'G' and (resid 44 through 140 )
25X-RAY DIFFRACTION25chain 'G' and (resid 141 through 150 )
26X-RAY DIFFRACTION26chain 'G' and (resid 151 through 163 )
27X-RAY DIFFRACTION27chain 'G' and (resid 164 through 175 )
28X-RAY DIFFRACTION28chain 'H' and (resid 6 through 94 )
29X-RAY DIFFRACTION29chain 'H' and (resid 95 through 150 )
30X-RAY DIFFRACTION30chain 'H' and (resid 151 through 174 )

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