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- PDB-9gyb: Crystal structure of the recombinant CODH from Rhodopspirillum ru... -

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Basic information

Entry
Database: PDB / ID: 9gyb
TitleCrystal structure of the recombinant CODH from Rhodopspirillum rubrum produced in Escherichia coli
ComponentsCarbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / Carbon monoxide dehydrogenase Redox nickel enzyme Electron transfer
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / ferrous iron binding / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding ...anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / hydroxylamine reductase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / ferrous iron binding / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / protein homodimerization activity / protein-containing complex / plasma membrane / cytoplasm
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(3)-Ni(1)-S(4) cluster / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCavazza, C. / Contaldo, U.
Funding support France, 1items
OrganizationGrant numberCountry
French Alternative Energies and Atomic Energy Commission (CEA) France
CitationJournal: Chemistry / Year: 2025
Title: Insights into the Role of the D-Cluster in [NiFe]-CODH from Rhodospirillum Rubrum.
Authors: Contaldo, U. / Guigliarelli, B. / Perard, J. / Pichon, T. / Le Goff, A. / Cavazza, C.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)407,21822
Polymers401,5686
Non-polymers5,65016
Water00
1
A: Carbon monoxide dehydrogenase
B: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7327
Polymers133,8562
Non-polymers1,8765
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-93 kcal/mol
Surface area37240 Å2
MethodPISA
2
C: Carbon monoxide dehydrogenase
D: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7558
Polymers133,8562
Non-polymers1,8996
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-98 kcal/mol
Surface area37380 Å2
MethodPISA
3
E: Carbon monoxide dehydrogenase
F: Carbon monoxide dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7327
Polymers133,8562
Non-polymers1,8765
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-93 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.450, 200.573, 116.370
Angle α, β, γ (deg.)90.000, 111.210, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Carbon monoxide dehydrogenase / CODH


Mass: 66927.969 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: cooS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P31896, anaerobic carbon monoxide dehydrogenase
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-RQM / Fe(3)-Ni(1)-S(4) cluster


Mass: 410.333 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4NiS4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, pH 7.5, 1 mM DTT, 10% PEG8000, 8% MPD, 0.2 M CaCl2.
PH range: 6.56-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.9→47.71 Å / Num. obs: 86518 / % possible obs: 99.11 % / Redundancy: 1.77 % / Biso Wilson estimate: 80.9 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.18
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 8126 / CC1/2: 0.13 / % possible all: 93.57

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.71 Å / SU ML: 0.6041 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2879 1100 1.27 %
Rwork0.2274 85377 -
obs0.2282 86477 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.96 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27189 0 127 0 27316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003827861
X-RAY DIFFRACTIONf_angle_d0.874438177
X-RAY DIFFRACTIONf_chiral_restr0.04664511
X-RAY DIFFRACTIONf_plane_restr0.00554890
X-RAY DIFFRACTIONf_dihedral_angle_d6.33293988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.39821310.364310163X-RAY DIFFRACTION94.84
3.03-3.190.32811380.339210744X-RAY DIFFRACTION99.95
3.19-3.390.33821380.294310711X-RAY DIFFRACTION99.88
3.39-3.650.31821380.246810717X-RAY DIFFRACTION99.82
3.65-4.020.28831390.219410775X-RAY DIFFRACTION99.84
4.02-4.60.2811380.191510749X-RAY DIFFRACTION99.84
4.6-5.80.29021390.213810768X-RAY DIFFRACTION99.83
5.8-47.710.2441390.196910750X-RAY DIFFRACTION98.91

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