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- PDB-6b6v: Crystal structure of Desulfovibrio vulgaris carbon monoxide dehyd... -

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Basic information

Entry
Database: PDB / ID: 6b6v
TitleCrystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated (protein batch 1), canonical C-cluster
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: 2.5 Å
AuthorsWittenborn, E.C. / Drennan, C.L.
Funding support United States, 2items
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)T32 GM008334 United States
CitationJournal: Elife / Year: 2018
Title: Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase.
Authors: Wittenborn, E.C. / Merrouch, M. / Ueda, C. / Fradale, L. / Leger, C. / Fourmond, V. / Pandelia, M.E. / Dementin, S. / Drennan, C.L.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,77614
Polymers135,4322
Non-polymers2,34412
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-147 kcal/mol
Surface area36340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.650, 111.960, 195.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 67715.898 Da / Num. of mol.: 2
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 , 5 types, 287 molecules

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


Mass: 351.640 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0-1.1 M ammonium tartrate dibasic, pH 7, 6-9% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2014
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: 2.5→100 Å / Num. obs: 50328 / % possible obs: 99.3 % / Redundancy: 4.2 % / Rsym value: 0.129 / Net I/σ(I): 9.8
Reflection shellResolution: 2.5→2.55 Å / Rsym value: 0.697

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JQK

1jqk


Resolution: 2.5→97.13 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.2057 2185 4.34 %
Rwork0.161 --
obs0.163 50322 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→97.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9241 0 80 275 9596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049504
X-RAY DIFFRACTIONf_angle_d0.94512962
X-RAY DIFFRACTIONf_dihedral_angle_d20.7435772
X-RAY DIFFRACTIONf_chiral_restr0.0421498
X-RAY DIFFRACTIONf_plane_restr0.0041682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55440.28571340.2322946X-RAY DIFFRACTION99
2.5544-2.61380.29651340.21472974X-RAY DIFFRACTION99
2.6138-2.67920.26981360.20712958X-RAY DIFFRACTION99
2.6792-2.75160.27291350.20722999X-RAY DIFFRACTION100
2.7516-2.83260.25761340.18592966X-RAY DIFFRACTION99
2.8326-2.9240.24451350.18632957X-RAY DIFFRACTION99
2.924-3.02850.22741340.17573003X-RAY DIFFRACTION99
3.0285-3.14980.22321390.17492960X-RAY DIFFRACTION99
3.1498-3.29310.25051320.17133012X-RAY DIFFRACTION100
3.2931-3.46680.21261390.15433009X-RAY DIFFRACTION100
3.4668-3.6840.20221350.14253009X-RAY DIFFRACTION99
3.684-3.96840.16911360.13732982X-RAY DIFFRACTION99
3.9684-4.36780.14731380.13053031X-RAY DIFFRACTION99
4.3678-4.99980.171400.12883062X-RAY DIFFRACTION100
4.9998-6.29910.19691380.16663059X-RAY DIFFRACTION99
6.2991-97.20340.18651460.1583210X-RAY DIFFRACTION98
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)
10.5768-0.05820.18520.58920.06130.80870.0175-0.1419-0.05840.1275-0.0256-0.03080.1388-0.0670.00980.2479-0.02280.0020.19340.00150.2733-0.9135-4.2092-4.1947
20.59320.04510.00370.5896-0.05240.64510.02110.06350.0393-0.1163-0.01990.0031-0.041-0.1520.00050.27360.01910.02240.2716-0.01670.2769-19.563313.9904-32.7522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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