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- PDB-6ond: Crystal structure of Desulfovibrio vulgaris carbon monoxide dehyd... -

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Basic information

Entry
Database: PDB / ID: 6ond
TitleCrystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, reduced
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / nickel-iron-sulfur (Ni-Fe-S) cluster / iron-sulfur (Fe-S) cluster / metalloenzyme
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / hydroxylamine reductase activity / anaerobic carbon-monoxide dehydrogenase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.723 Å
AuthorsWittenborn, E.C. / Cohen, S.E. / Drennan, C.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008334 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase.
Authors: Wittenborn, E.C. / Cohen, S.E. / Merrouch, M. / Leger, C. / Fourmond, V. / Dementin, S. / Drennan, C.L.
History
DepositionApr 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
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.ptnr1_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
C: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,92631
Polymers270,8644
Non-polymers4,06227
Water34,2101899
1
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,45816
Polymers135,4322
Non-polymers2,02614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-224 kcal/mol
Surface area36380 Å2
MethodPISA
2
C: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,46815
Polymers135,4322
Non-polymers2,03613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-201 kcal/mol
Surface area36310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.790, 144.150, 123.690
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbon monoxide dehydrogenase


Mass: 67715.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Gene: cooS, DVU_2098 / Production host: Desulfovibrio fructosivorans (bacteria)
References: UniProt: Q72A99, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 8 types, 1926 molecules

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


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1899 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 200-275 mM magnesium chloride, 14-20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 4, 2017
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.72→100 Å / Num. obs: 225437 / % possible obs: 95.9 % / Redundancy: 5.1 % / Rsym value: 0.093 / Net I/σ(I): 11.3
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 16599 / Rsym value: 0.913

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B6V

6b6v


Resolution: 1.723→93.272 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.25
RfactorNum. reflection% reflection
Rfree0.1762 11415 5.06 %
Rwork0.1494 --
obs0.1508 225376 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.723→93.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18436 0 94 1899 20429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719115
X-RAY DIFFRACTIONf_angle_d0.91926074
X-RAY DIFFRACTIONf_dihedral_angle_d26.2657021
X-RAY DIFFRACTIONf_chiral_restr0.0793040
X-RAY DIFFRACTIONf_plane_restr0.0053435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7226-1.74220.28953220.25766060X-RAY DIFFRACTION81
1.7422-1.76270.27353740.24157153X-RAY DIFFRACTION96
1.7627-1.78420.2483770.22987044X-RAY DIFFRACTION95
1.7842-1.80680.2773710.22347030X-RAY DIFFRACTION94
1.8068-1.83050.24333540.19786654X-RAY DIFFRACTION90
1.8305-1.85560.21623790.18177174X-RAY DIFFRACTION96
1.8556-1.88210.22423860.17577244X-RAY DIFFRACTION97
1.8821-1.91020.22063830.16757163X-RAY DIFFRACTION96
1.9102-1.94010.19353830.16667237X-RAY DIFFRACTION98
1.9401-1.97190.21493840.167245X-RAY DIFFRACTION96
1.9719-2.00590.18493850.14847221X-RAY DIFFRACTION97
2.0059-2.04240.19493830.15017229X-RAY DIFFRACTION97
2.0424-2.08160.19253940.14717267X-RAY DIFFRACTION97
2.0816-2.12410.18663860.14397202X-RAY DIFFRACTION97
2.1241-2.17030.18693810.14637209X-RAY DIFFRACTION96
2.1703-2.22080.18343910.14257222X-RAY DIFFRACTION97
2.2208-2.27640.17853880.14377006X-RAY DIFFRACTION95
2.2764-2.33790.19343380.14686638X-RAY DIFFRACTION88
2.3379-2.40670.17453690.14347323X-RAY DIFFRACTION98
2.4067-2.48440.1813850.14697335X-RAY DIFFRACTION98
2.4844-2.57320.17554070.1437336X-RAY DIFFRACTION98
2.5732-2.67620.18024220.14737277X-RAY DIFFRACTION98
2.6762-2.7980.17823980.14617291X-RAY DIFFRACTION98
2.798-2.94560.19414030.14827301X-RAY DIFFRACTION97
2.9456-3.13010.16423690.1487240X-RAY DIFFRACTION97
3.1301-3.37180.16623680.14246650X-RAY DIFFRACTION89
3.3718-3.71110.1463910.13277340X-RAY DIFFRACTION98
3.7111-4.24820.13343850.12457419X-RAY DIFFRACTION98
4.2482-5.35220.13043830.12977341X-RAY DIFFRACTION97
5.3522-93.40940.17313760.16077110X-RAY DIFFRACTION93
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)
10.3034-0.08990.00170.39-0.03380.13370.01880.0471-0.0608-0.0549-0.0026-0.02380.01970.0254-0.01350.1394-0.001-0.00810.1578-0.01420.17125.66772.0343.4265
20.2993-0.02830.08370.34730.02540.1908-0.01130.00130.0624-0.01520.02040.0219-0.0329-0.0144-0.00750.13580.0026-0.00010.15310.0150.184-12.513635.506150.0559
30.29370.01660.01610.37060.03750.23090.01690.0418-0.0456-0.05390.0291-0.05360.02090.0558-0.04290.1350.0028-0.00730.1801-0.030.1687-17.86734.8041-18.8992
40.2750.03560.04630.61230.02670.26230.0145-0.01740.07550.01360.0190.1085-0.06290.0222-0.0330.137-0.00590.0130.14890.00670.1923-36.16637.6274-9.9403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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