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- PDB-9iyn: ChCODH2 A559H_V610H mutant -

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Basic information

Entry
Database: PDB / ID: 9iyn
TitleChCODH2 A559H_V610H mutant
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: 1.83 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)70,2925
Polymers69,2981
Non-polymers9944
Water6,053336
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,58310
Polymers138,5962
Non-polymers1,9878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8470 Å2
ΔGint-127 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.867, 75.311, 70.948
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1078-

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: 69297.977 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

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Non-polymers , 5 types, 340 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
#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.: 336 / 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: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 47694 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.9
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.719 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SU7

1su7


Resolution: 1.83→35.22 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 2176 4.91 %
Rwork0.168 --
obs0.17 44355 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 22 336 5019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094770
X-RAY DIFFRACTIONf_angle_d1.0926492
X-RAY DIFFRACTIONf_dihedral_angle_d6.422671
X-RAY DIFFRACTIONf_chiral_restr0.062782
X-RAY DIFFRACTIONf_plane_restr0.009838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.870.2967740.27311654X-RAY DIFFRACTION57
1.87-1.910.26761080.23671939X-RAY DIFFRACTION68
1.91-1.960.28951120.21322166X-RAY DIFFRACTION77
1.96-2.010.26131470.20182403X-RAY DIFFRACTION85
2.01-2.070.25291380.19652640X-RAY DIFFRACTION92
2.07-2.140.23711490.18462762X-RAY DIFFRACTION97
2.14-2.220.26511540.17722850X-RAY DIFFRACTION99
2.22-2.310.24441460.17362818X-RAY DIFFRACTION99
2.31-2.410.23291370.16312910X-RAY DIFFRACTION100
2.41-2.540.22641530.16412848X-RAY DIFFRACTION100
2.54-2.70.19651390.16422884X-RAY DIFFRACTION100
2.7-2.910.21111260.16812871X-RAY DIFFRACTION100
2.91-3.20.23891500.17562868X-RAY DIFFRACTION99
3.2-3.660.21651370.15832842X-RAY DIFFRACTION99
3.66-4.610.16211500.13722828X-RAY DIFFRACTION97
4.61-35.220.20831560.1552896X-RAY DIFFRACTION98

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