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- PDB-6vwy: Crystal structure of C45G/T50C D. vulgaris carbon monoxide dehydr... -

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Basic information

Entry
Database: PDB / ID: 6vwy
TitleCrystal structure of C45G/T50C D. vulgaris carbon monoxide dehydrogenase (anaerobic)
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
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
Similarity search - Domain/homology
Fe(4)-Ni(1)-S(4) cluster, oxidized / 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: 1.83 Å
AuthorsWittenborn, E.C. / Drennan, C.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008334 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acs Catalysis / Year: 2020
Title: The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance inDesulfovibrio vulgarisNi-Fe Carbon Monoxide Dehydrogenase.
Authors: Wittenborn, E.C. / Guendon, C. / Merrouch, M. / Benvenuti, M. / Fourmond, V. / Leger, C. / Drennan, C.L. / Dementin, S.
History
DepositionFeb 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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)136,57014
Polymers133,4132
Non-polymers3,15712
Water14,466803
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-92 kcal/mol
Surface area35810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.560, 147.360, 66.050
Angle α, β, γ (deg.)90.000, 110.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbon monoxide dehydrogenase


Mass: 66706.711 Da / Num. of mol.: 2 / Mutation: C45G/T50C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: cooS, DVU_2098 / Production host: Desulfovibrio fructosivorans JJ (bacteria)
References: UniProt: Q72A99, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 5 types, 815 molecules

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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#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
#4: Chemical ChemComp-CUV / Fe(4)-Ni(1)-S(4) cluster, oxidized / C cluster, oxidized


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 803 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 150-250 mM magnesium chloride, 16-20% w/v 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 / Detector: PIXEL / Date: Apr 8, 2016
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: 1.83→100 Å / Num. obs: 102654 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 13.8
Reflection shellResolution: 1.83→1.87 Å / Num. unique obs: 7601 / CC1/2: 0.829

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B6V

6b6v


Resolution: 1.83→73.68 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.32
RfactorNum. reflection% reflection
Rfree0.1776 5131 5 %
Rwork0.1472 --
obs0.1487 102640 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.71 Å2 / Biso mean: 29.9732 Å2 / Biso min: 15.64 Å2
Refinement stepCycle: final / Resolution: 1.83→73.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9191 0 90 803 10084
Biso mean--31.39 39.79 -
Num. residues----1251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.83-1.85080.28681690.25693206100
1.8508-1.87260.28481730.23523290100
1.8726-1.89540.24851680.20883204100
1.8954-1.91940.25411730.20243271100
1.9194-1.94470.24011710.18493252100
1.9447-1.97130.24571690.18223239100
1.9713-1.99950.2451710.1713245100
1.9995-2.02930.22111700.16963228100
2.0293-2.0610.21951720.15833266100
2.061-2.09480.18391690.15793218100
2.0948-2.1310.20431720.15113267100
2.131-2.16970.19611700.15323232100
2.1697-2.21140.22161720.14723260100
2.2114-2.25660.17631720.14073266100
2.2566-2.30570.20611690.14193207100
2.3057-2.35930.20291720.14763264100
2.3593-2.41830.18911720.14463270100
2.4183-2.48370.17711700.13853227100
2.4837-2.55680.16551700.14123238100
2.5568-2.63930.20561720.14413270100
2.6393-2.73360.18851710.14023249100
2.7336-2.84310.17411710.14173249100
2.8431-2.97250.16651720.14443255100
2.9725-3.12920.18781710.14013261100
3.1292-3.32530.15631700.1355322599
3.3253-3.5820.15431720.13363272100
3.582-3.94240.14151710.1243256100
3.9424-4.51290.14151710.12283245100
4.5129-5.68540.16171730.148327799
5.6854-73.680.15241730.1597330099
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)
10.34840.0342-0.05660.95030.12360.3963-0.0157-0.01970.0690.08860.02020.0024-0.08660.0148-0.00420.24580.00450.03260.18960.00480.193120.7632-0.2411-0.3083
20.36480.1521-0.02250.5810.11490.3696-0.06930.0519-0.1496-0.14120.0608-0.08290.0330.01410.01430.2422-0.0240.07210.2034-0.01540.245321.7828-33.2814-20.0837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or chain M or chain NA4 - 629
2X-RAY DIFFRACTION1chain A or chain M or chain NM800
3X-RAY DIFFRACTION1chain A or chain M or chain NN800
4X-RAY DIFFRACTION2chain B or chain O or chain PB4 - 628
5X-RAY DIFFRACTION2chain B or chain O or chain PO800
6X-RAY DIFFRACTION2chain B or chain O or chain PP800

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