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- PDB-9iyv: ChCODH2 WT in 2hour air exposure condition -

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Basic information

Entry
Database: PDB / ID: 9iyv
TitleChCODH2 WT in 2hour air exposure condition
ComponentsCarbon monoxide dehydrogenase 2
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT
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 / 4 iron, 4 sulfur cluster binding / 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
: / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKong, S.Y. / Yoon, H.J. / Kim, S.M. / Lee, H.H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Air-viable, rapid CO dehydrogenase with a selectively sealed tunnel
Authors: Kong, S.Y. / Yoon, H.J. / Kim, S.M. / Lee, H.H.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7676
Polymers69,1921
Non-polymers5755
Water27015
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,53412
Polymers138,3842
Non-polymers1,15010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9040 Å2
ΔGint-200 kcal/mol
Surface area37730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.941, 76.028, 71.124
Angle α, β, γ (deg.)90.00, 111.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69191.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Magnesium chloride, Hepes/NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19232 / % possible obs: 98.7 % / Redundancy: 6.08 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.042 / Net I/σ(I): 26.41
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.5-2.650.33430630.9650.3641
2.65-2.830.21628990.9830.2351
2.83-3.050.13226900.9950.1441
3.05-3.340.07824810.9970.0861
3.34-3.740.04622990.9990.051
3.74-4.310.0319760.9990.0331
4.31-5.260.02517040.9990.0271
5.26-7.380.02713470.9990.031
7.38-500.0237730.9990.0251

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SU7

1su7


Resolution: 2.5→34.15 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 962 5 %
Rwork0.1925 --
obs0.1962 19221 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→34.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 12 15 4680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084737
X-RAY DIFFRACTIONf_angle_d0.9446442
X-RAY DIFFRACTIONf_dihedral_angle_d6.128662
X-RAY DIFFRACTIONf_chiral_restr0.055778
X-RAY DIFFRACTIONf_plane_restr0.008834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.32881340.23862551X-RAY DIFFRACTION98
2.63-2.790.2741360.20882584X-RAY DIFFRACTION99
2.79-3.010.30021370.22472599X-RAY DIFFRACTION99
3.01-3.310.30681380.21062604X-RAY DIFFRACTION99
3.31-3.790.29761370.19962610X-RAY DIFFRACTION99
3.79-4.770.22261380.17112629X-RAY DIFFRACTION99
4.77-34.150.25161420.1852682X-RAY DIFFRACTION100

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