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- PDB-9iyl: ChCODH2 WT -

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Basic information

Entry
Database: PDB / ID: 9iyl
TitleChCODH2 WT
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: 1.28 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 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 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)70,1865
Polymers69,1921
Non-polymers9944
Water8,899494
1
A: Carbon monoxide dehydrogenase 2
hetero molecules

A: Carbon monoxide dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,37110
Polymers138,3842
Non-polymers1,9878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8470 Å2
ΔGint-122 kcal/mol
Surface area38040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.940, 75.800, 71.650
Angle α, β, γ (deg.)90.00, 111.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1212-

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: 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

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Non-polymers , 5 types, 498 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.: 494 / 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: 2.01 Å3/Da / Density % sol: 38.95 %
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: 0.999994 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999994 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 137315 / % possible obs: 96.3 % / Redundancy: 4.67 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.049 / Net I/σ(I): 7.51
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.28-1.360.3695200.770.5091
1.36-1.450.23397210.8790.3291
1.45-1.570.14187960.950.1991
1.57-1.720.08578940.9790.1211
1.72-1.920.0668810.9890.0851
1.92-2.220.04455370.9930.0631
2.22-2.710.0356590.9960.0431
2.71-3.830.02542430.9970.0361
3.83-500.02320860.9970.0321

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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: 1.28→37.9 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 6861 5 %
Rwork0.1753 --
obs0.1763 137179 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4675 0 0 494 5169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084760
X-RAY DIFFRACTIONf_angle_d1.0886479
X-RAY DIFFRACTIONf_dihedral_angle_d6.115671
X-RAY DIFFRACTIONf_chiral_restr0.086783
X-RAY DIFFRACTIONf_plane_restr0.01836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.290.33171150.3022183X-RAY DIFFRACTION48
1.29-1.310.28882280.27994324X-RAY DIFFRACTION94
1.31-1.320.28432250.26014276X-RAY DIFFRACTION95
1.32-1.340.28992260.25094284X-RAY DIFFRACTION95
1.34-1.360.27362280.23824339X-RAY DIFFRACTION95
1.36-1.370.25112310.2294376X-RAY DIFFRACTION95
1.37-1.390.24432240.22324268X-RAY DIFFRACTION95
1.39-1.420.23522300.21514354X-RAY DIFFRACTION96
1.42-1.440.22042320.21334413X-RAY DIFFRACTION96
1.44-1.460.22542290.2064350X-RAY DIFFRACTION96
1.46-1.490.22992290.20044359X-RAY DIFFRACTION96
1.49-1.510.20342310.19134376X-RAY DIFFRACTION96
1.51-1.540.21622310.18524392X-RAY DIFFRACTION96
1.54-1.570.20162330.18164422X-RAY DIFFRACTION96
1.57-1.610.22152320.17964416X-RAY DIFFRACTION97
1.61-1.650.22922300.17524388X-RAY DIFFRACTION97
1.65-1.690.19942320.1734402X-RAY DIFFRACTION97
1.69-1.730.21032330.17774442X-RAY DIFFRACTION97
1.73-1.780.17832340.17094440X-RAY DIFFRACTION97
1.78-1.840.21742340.17274432X-RAY DIFFRACTION97
1.84-1.910.18642330.16794433X-RAY DIFFRACTION98
1.91-1.980.17712360.16344470X-RAY DIFFRACTION98
1.98-2.070.19342330.16874446X-RAY DIFFRACTION97
2.07-2.180.17542360.16474472X-RAY DIFFRACTION97
2.18-2.320.17222340.17124443X-RAY DIFFRACTION97
2.32-2.50.18242380.16814513X-RAY DIFFRACTION99
2.5-2.750.19582400.17514538X-RAY DIFFRACTION99
2.75-3.150.18772380.17724551X-RAY DIFFRACTION99
3.15-3.960.17782420.16054599X-RAY DIFFRACTION99
3.96-37.90.18182440.15794617X-RAY DIFFRACTION99

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