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- PDB-7tsj: Xenon-bound structure of carbon monoxide dehydrogenase (CODH) fro... -

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Basic information

Entry
Database: PDB / ID: 7tsj
TitleXenon-bound structure of carbon monoxide dehydrogenase (CODH) from Desulfovibrio vulgaris
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / CO-dehydrogenase / Desulfovibrio vulgaris / Xenon
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 / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / XENON / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBiester, A. / Drennan, C.L.
Funding support United States, Canada, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
Canadian Institute for Advanced Research (CIFAR) Canada
CitationJournal: J.Inorg.Biochem. / Year: 2022
Title: Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase.
Authors: Biester, A. / Dementin, S. / Drennan, C.L.
History
DepositionJan 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,22916
Polymers67,7161
Non-polymers2,51315
Water1,33374
1
A: Carbon monoxide dehydrogenase
hetero molecules

A: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,45832
Polymers135,4322
Non-polymers5,02730
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13680 Å2
ΔGint-119 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.892, 100.870, 65.384
Angle α, β, γ (deg.)90.000, 124.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbon monoxide dehydrogenase


Mass: 67715.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Gene: cooS, DVU_2098
Production host: Solidesulfovibrio fructosivorans (bacteria)
References: UniProt: Q72A99, anaerobic carbon monoxide dehydrogenase

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Non-polymers , 5 types, 89 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe2S2
#4: Chemical ChemComp-CUV / Fe(4)-Ni(1)-S(4) cluster, oxidized / C cluster, oxidized


Mass: 410.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe4NiS4
#5: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 250 mM MgCl2, 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→46.72 Å / Num. obs: 34865 / % possible obs: 97.7 % / Redundancy: 3.867 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.071 / Χ2: 0.786 / Net I/σ(I): 12.57 / Num. measured all: 134825
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.233.6730.4752.8820657573656240.8920.54798
2.23-2.384.040.3194.6121564540653380.9540.36398.7
2.38-2.573.980.1996.8719621498549300.980.22798.9
2.57-2.813.9140.139.8517878465845680.9880.14998.1
2.81-3.143.6140.08413.9514628417340480.9940.09797
3.14-3.634.070.05721.2914867374636530.9960.06597.5
3.63-4.443.9410.04626.2912007312730470.9970.05397.4
4.44-6.243.6030.04327.398421244123370.9960.0595.7
6.24-46.723.9260.04330.565182142313200.9960.04992.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B6V

6b6v


Resolution: 2.1→46.72 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 1818 5.22 %
Rwork0.1668 33029 -
obs0.1689 34847 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.93 Å2 / Biso mean: 52.9908 Å2 / Biso min: 27.87 Å2
Refinement stepCycle: final / Resolution: 2.1→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 0 31 74 4705
Biso mean--49.07 50.5 -
Num. residues----621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.29421280.2322507263596
2.15-2.220.25621580.20682525268399
2.22-2.290.25241360.19712572270899
2.29-2.370.23711450.19062560270599
2.37-2.470.24211400.18542559269999
2.47-2.580.24131350.1862548268399
2.58-2.710.23191480.18392588273699
2.71-2.880.26021270.18992500262798
2.88-3.110.22751370.20072524266197
3.11-3.420.22011420.18072547268998
3.42-3.910.19781420.15892530267298
3.91-4.930.1881440.13912541268598
4.93-46.720.15411360.14422528266495
Refinement TLS params.Method: refined / Origin x: 19.232 Å / Origin y: -5.7906 Å / Origin z: 1.5046 Å
111213212223313233
T0.3096 Å20.0199 Å20.0203 Å2-0.3464 Å20.0345 Å2--0.3812 Å2
L2.0368 °2-0.2473 °2-0.2138 °2-1.0751 °2-0.0783 °2--0.8442 °2
S0.0659 Å °-0.2058 Å °-0.1212 Å °0.1203 Å °-0.1225 Å °-0.1952 Å °0.1328 Å °0.2087 Å °0.0528 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 793
2X-RAY DIFFRACTION1allA893 - 1011

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