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- PDB-9iyu: ChCODH2 A559W_V610H mutant in 24hour air exposure condition -

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Basic information

Entry
Database: PDB / ID: 9iyu
TitleChCODH2 A559W_V610H mutant in 24hour 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
: / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

Deposited unit
A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3405
Polymers69,3461
Non-polymers9944
Water3,225179
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,67910
Polymers138,6922
Non-polymers1,9878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8410 Å2
ΔGint-123 kcal/mol
Surface area37450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.638, 76.281, 72.084
Angle α, β, γ (deg.)90.00, 112.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-961-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbon monoxide dehydrogenase 2 / CODH 2


Mass: 69346.039 Da / Num. of mol.: 1 / Mutation: A559W,V610H
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

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Non-polymers , 5 types, 183 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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→50 Å / Num. obs: 38166 / % possible obs: 99 % / Redundancy: 3.12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.044 / Net I/σ(I): 8.55
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.120.23730470.90.3231
2.12-2.270.15828580.9490.2141
2.27-2.450.09126570.9820.1231
2.45-2.680.06323540.990.0851
2.68-2.990.04220510.9950.0571
2.99-3.450.03117790.9960.0421
3.45-4.220.02415080.9980.0321
4.22-5.940.02511000.9970.0331
5.94-500.0265670.9980.0351

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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→35.08 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1903 5 %
Rwork0.1857 --
obs0.1875 38066 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 0 179 4866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114775
X-RAY DIFFRACTIONf_angle_d1.1926500
X-RAY DIFFRACTIONf_dihedral_angle_d6.473671
X-RAY DIFFRACTIONf_chiral_restr0.065782
X-RAY DIFFRACTIONf_plane_restr0.013838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33581320.26082515X-RAY DIFFRACTION98
2.05-2.10.3081350.28412567X-RAY DIFFRACTION99
2.1-2.170.2551350.20452573X-RAY DIFFRACTION100
2.17-2.240.24491340.22942549X-RAY DIFFRACTION99
2.24-2.320.3731330.2852520X-RAY DIFFRACTION97
2.32-2.410.25991370.18962598X-RAY DIFFRACTION100
2.41-2.520.22721360.19712587X-RAY DIFFRACTION100
2.52-2.650.24561350.19742571X-RAY DIFFRACTION100
2.65-2.820.26191370.20232606X-RAY DIFFRACTION100
2.82-3.030.26481370.21322591X-RAY DIFFRACTION100
3.03-3.340.23061360.19632593X-RAY DIFFRACTION100
3.34-3.820.21581370.17512610X-RAY DIFFRACTION99
3.82-4.810.16111380.13972622X-RAY DIFFRACTION100
4.81-35.080.16921410.15472661X-RAY DIFFRACTION100

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