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- PDB-4z3z: Active site complex BamBC of Benzoyl Coenzyme A reductase in comp... -

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Basic information

Entry
Database: PDB / ID: 4z3z
TitleActive site complex BamBC of Benzoyl Coenzyme A reductase in complex with Zinc
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
Chem-MTE / 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: 2.666 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

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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)386,14348
Polymers376,1188
Non-polymers10,02540
Water00
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)193,07124
Polymers188,0594
Non-polymers5,01320
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19040 Å2
ΔGint-331 kcal/mol
Surface area57160 Å2
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)193,07124
Polymers188,0594
Non-polymers5,01320
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18620 Å2
ΔGint-329 kcal/mol
Surface area57590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.240, 117.430, 143.080
Angle α, β, γ (deg.)90.00, 111.04, 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 / Benzoyl coenzyme A reductase subunit B


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 / Benzoyl coenzyme A reductase subunit C


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

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Non-polymers , 6 types, 40 molecules

#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 35.453 Da / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3.8 % PEG 4000 0.2 M LiCl 2 mM DTT 1 mM ZnSO4 0.2 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.666→82.511 Å / Num. all: 109678 / Num. obs: 106725 / % possible obs: 97.3 % / Redundancy: 3.96 % / Rsym value: 0.14 / Net I/σ(I): 6.68
Reflection shellResolution: 2.666→2.73 Å / Redundancy: 3.88 % / Rmerge(I) obs: 1.69 / Mean I/σ(I) obs: 0.95 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z40

4z40


Resolution: 2.666→82.511 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 1389 1.3 %
Rwork0.2315 --
obs0.232 106469 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.666→82.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25790 0 336 0 26126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826932
X-RAY DIFFRACTIONf_angle_d0.81436413
X-RAY DIFFRACTIONf_dihedral_angle_d13.08510149
X-RAY DIFFRACTIONf_chiral_restr0.0293887
X-RAY DIFFRACTIONf_plane_restr0.0034684
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5180X-RAY DIFFRACTIONPOSITIONAL
12B5180X-RAY DIFFRACTIONPOSITIONAL0.001
13C5180X-RAY DIFFRACTIONPOSITIONAL0.001
14D5180X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6657-2.7610.42631280.40279988X-RAY DIFFRACTION93
2.761-2.87150.3911410.373410444X-RAY DIFFRACTION97
2.8715-3.00220.39241380.350210492X-RAY DIFFRACTION98
3.0022-3.16050.34151380.306910560X-RAY DIFFRACTION98
3.1605-3.35850.35071450.288410586X-RAY DIFFRACTION98
3.3585-3.61780.30881330.273810552X-RAY DIFFRACTION98
3.6178-3.98190.27951390.233610609X-RAY DIFFRACTION98
3.9819-4.5580.2331410.202910593X-RAY DIFFRACTION98
4.558-5.74240.2381420.185210689X-RAY DIFFRACTION98
5.7424-82.55040.20921440.168410567X-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)
11.24580.0229-0.49951.1709-0.59530.6951.85130.74592.3166-0.8379-0.1241-0.667-1.9454-0.5231.14542.29330.49731.48230.45490.6682.1882-6.754357.6431.0775
20.1024-0.1080.24080.9042-0.52550.55261.16241.41221.4935-0.5898-0.4592-0.28-1.3953-1.6562-0.0142.86121.6231.63071.38221.98052.2289-13.633660.790116.6782
30.2998-0.56920.291.5188-0.42870.20270.3180.65951.0403-0.56060.03440.3337-0.6632-0.420.05912.21951.85471.05881.68311.33112.1762-32.142164.93927.289
42.1524-0.7099-1.39252.58181.21381.94970.02620.1621-0.1022-0.4614-0.1294-0.8294-0.0520.09130.10420.69790.12930.20220.52650.08190.9411-29.732955.742971.757
51.55480.3752-0.78122.83730.71181.94650.0062-0.5028-0.18610.4508-0.1453-0.40650.17960.11650.18460.40210.1097-0.15060.52710.05680.5559-35.50462.539495.9836
60.4437-0.2627-0.44161.66350.99791.724-0.3773-0.548-0.09190.05380.3285-0.90590.46650.960.04790.67140.30370.06921.05450.08211.5772-10.850150.652386.5613
70.83430.4614-0.29511.06030.02741.3588-0.51310.7103-1.15640.0714-0.29830.40010.7399-0.89190.00240.9409-0.56520.25491.1668-0.86991.1084-88.727425.329385.4628
81.86570.207-1.56261.12230.19822.3365-0.39980.2802-0.71810.4467-0.08840.76610.377-0.80450.17060.5131-0.276-0.03551.0646-0.37690.7321-95.366636.6259101.4247
91.91840.0139-1.08990.9323-0.40842.73160.2747-1.63150.07950.0597-0.1633-0.30980.06571.5378-0.09910.5536-0.0594-0.02011.0159-0.11860.568447.2323.467715.9931
101.3594-0.4569-1.80110.85671.01932.88141.00930.46661.0272-0.27360.2083-0.0536-1.78190.0763-1.04431.3229-0.05710.50720.7839-0.05131.388539.538447.8544-3.1897
111.56330.3-0.90371.1393-0.38872.1410.5627-0.38060.6338-0.19030.11-0.2716-0.86560.6501-0.00970.6656-0.25310.12270.6212-0.27810.668949.25737.1416-2.3984
120.36980.6989-0.02591.5351-0.52.83540.3223-1.28770.0515-0.0296-0.3268-0.42540.02572.1789-0.22190.6713-0.1820.09362.0614-0.26790.94267.547130.80728.5696
131.341-0.60480.02833.46350.39420.13080.1637-0.80840.61030.53650.07480.1177-0.60740.55270.18991.0365-0.4840.24351.685-0.59910.76237.515638.72935.5911
141.46640.2653-0.45160.5983-0.02560.21380.801-1.1040.51410.0756-0.026-0.097-0.45911.1143-0.31870.7429-0.17620.01260.962-0.22860.610626.313630.508932.8418
151.2770.11050.26440.4539-0.12040.09730.4122-0.63310.14730.09660.2537-0.19180.0450.30330.21471.3594-0.90070.38871.6572-0.6791.118234.279346.128440.5095
163.5359-0.6097-0.77113.3207-2.67892.62480.2536-0.24850.28410.27060.4129-0.2411-0.10240.0415-0.43071.4356-0.36570.08761.9436-0.21921.48231.956232.943956.6071
170.02570.0119-0.01120.02730.00230.00720.1262-1.3095-0.83090.80260.3929-0.16250.3950.0867-0.30641.507-0.198-0.03271.70150.38691.38195.220921.804860.833
182.8511-0.7635-2.01752.19971.01082.24061.0345-0.49761.1-0.38240.0613-0.7834-0.7880.6677-0.27570.6738-0.11140.02670.527-0.07130.54618.87835.57235.5227
191.3425-0.1314-0.6660.48-0.19741.22570.0908-0.6762-0.08910.1118-0.77470.01970.31950.1170.58611.3747-0.1666-0.07022.6011-0.26441.033912.201925.846954.4243
200.8487-0.1202-0.26141.0648-0.26551.2798-0.41620.5403-0.8344-0.7430.0986-0.23710.4016-0.49620.18930.798-0.13820.25730.6157-0.24631.0842-43.635334.860868.622
211.4262-0.42760.01011.13810.06510.84910.12830.862-0.2028-0.3194-0.2663-0.25490.3277-1.06250.03520.6742-0.13970.06281.0056-0.28890.649-57.452542.722169.2333
222.06230.1872-0.85340.5954-0.7423.06610.16961.2273-0.13-0.4443-0.2178-0.0230.1499-0.41240.29090.8366-0.06610.16731.251-0.17760.8651-54.902842.804663.8845
231.57770.8241-0.40482.55220.85380.6466-0.47760.6951-0.9421-0.5956-0.2402-0.26250.9576-0.34970.33841.1082-0.0820.45130.7906-0.30391.2607-43.084330.409964.0537
241.6208-0.7871-1.00681.5334-0.82492.1335-0.21540.7573-0.9638-0.1428-0.1186-0.14840.6048-0.51540.29761.0776-0.02010.39970.5709-0.04931.3063-49.190924.756376.2741
253.4928-1.55440.11422.18421.61521.90130.26220.0546-0.19630.1215-0.27870.20150.3359-0.29320.06771.3541-0.45690.42171.7883-0.69241.3404-60.619820.076259.3583
261.53831.8093-2.20786.8157-0.77696.68410.03060.4817-0.3304-0.3435-0.1280.32020.58880.05320.11821.311-0.34090.2781.863-0.76341.4231-52.184233.560847.7286
271.8538-1.1067-1.7140.8850.89461.6620.21180.4927-0.1863-0.3947-0.09590.02480.0656-0.1161-0.00181.7442-0.37560.06352.4882-0.44870.7606-48.588137.537137.0471
282.32331.1421-0.52543.0649-1.24840.84910.11250.88030.0385-0.3991-0.1994-0.1471-0.33570.59480.10890.75780.0294-0.20511.1646-0.16410.2433-65.780951.934161.3308
291.87110.47671.30260.70810.2990.9368-0.2070.9427-0.4283-0.4842-0.11120.14750.4395-0.50710.0870.8088-0.1571-0.03421.4622-0.39640.7167-78.207237.144971.9075
302.5884-0.78081.56531.40060.17451.8261-0.18931.2401-0.5425-0.5203-0.3420.0010.2173-0.35290.4720.8629-0.14420.1350.9133-0.36990.9342-61.936433.855471.2151
312.39120.71240.71390.8835-0.39480.7915-0.01271.1911-1.0141-0.3044-0.3772-0.18980.2143-0.32040.02090.9086-0.1870.11.5788-0.48390.7174-72.01236.224865.8175
323.5854-0.7822-2.64032.3487-0.08492.1504-0.13290.76010.2421-0.5866-0.2921-0.3001-0.5957-0.36880.21270.8124-0.1034-0.27121.2381-0.05430.418-66.586351.916464.6462
332.91211.51441.52930.79580.81150.8188-0.04880.7679-0.3164-0.1366-0.0683-0.43610.22130.12250.0551.5957-0.18380.4461.534-0.27640.9018-43.83332.061544.4433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 297 )
2X-RAY DIFFRACTION2chain 'A' and (resid 298 through 564 )
3X-RAY DIFFRACTION3chain 'A' and (resid 565 through 652 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 257 )
5X-RAY DIFFRACTION5chain 'B' and (resid 258 through 416 )
6X-RAY DIFFRACTION6chain 'B' and (resid 417 through 652 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 257 )
8X-RAY DIFFRACTION8chain 'C' and (resid 258 through 652 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 257 )
10X-RAY DIFFRACTION10chain 'D' and (resid 258 through 297 )
11X-RAY DIFFRACTION11chain 'D' and (resid 298 through 510 )
12X-RAY DIFFRACTION12chain 'D' and (resid 511 through 652 )
13X-RAY DIFFRACTION13chain 'E' and (resid 7 through 43 )
14X-RAY DIFFRACTION14chain 'E' and (resid 44 through 114 )
15X-RAY DIFFRACTION15chain 'E' and (resid 115 through 149 )
16X-RAY DIFFRACTION16chain 'E' and (resid 150 through 163 )
17X-RAY DIFFRACTION17chain 'E' and (resid 164 through 174 )
18X-RAY DIFFRACTION18chain 'F' and (resid 7 through 140 )
19X-RAY DIFFRACTION19chain 'F' and (resid 141 through 176 )
20X-RAY DIFFRACTION20chain 'G' and (resid 7 through 54 )
21X-RAY DIFFRACTION21chain 'G' and (resid 55 through 84 )
22X-RAY DIFFRACTION22chain 'G' and (resid 85 through 104 )
23X-RAY DIFFRACTION23chain 'G' and (resid 105 through 127 )
24X-RAY DIFFRACTION24chain 'G' and (resid 128 through 140 )
25X-RAY DIFFRACTION25chain 'G' and (resid 141 through 150 )
26X-RAY DIFFRACTION26chain 'G' and (resid 151 through 162 )
27X-RAY DIFFRACTION27chain 'G' and (resid 163 through 175 )
28X-RAY DIFFRACTION28chain 'H' and (resid 6 through 15 )
29X-RAY DIFFRACTION29chain 'H' and (resid 16 through 57 )
30X-RAY DIFFRACTION30chain 'H' and (resid 58 through 84 )
31X-RAY DIFFRACTION31chain 'H' and (resid 85 through 127 )
32X-RAY DIFFRACTION32chain 'H' and (resid 128 through 151 )
33X-RAY DIFFRACTION33chain 'H' and (resid 152 through 174 )

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