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Open data
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Basic information
Entry | Database: PDB / ID: 9iym | ||||||
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Title | ChCODH2 A559W_V610H mutant | ||||||
![]() | Carbon monoxide dehydrogenase 2 | ||||||
![]() | OXIDOREDUCTASE / ELECTRON TRANSPORT | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kong, S.Y. / Yoon, H.J. / Kim, S.M. / Lee, H.H. | ||||||
Funding support | 1items
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.1 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.3 KB | Display | ![]() |
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Full document | ![]() | 482.9 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9iylC ![]() 9iynC ![]() 9iyoC ![]() 9iyrC ![]() 9iysC ![]() 9iytC ![]() 9iyuC ![]() 9iyvC ![]() 1su7S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 69346.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Production host: ![]() ![]() References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase |
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-Non-polymers , 5 types, 317 molecules 








#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-FES / |
#4: Chemical | ChemComp-XCC / |
#5: Chemical | ChemComp-FE / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.81 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Magnesium chloride, Hepes/NaOH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. obs: 50080 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.82→1.85 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.889 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SU7 Resolution: 1.82→37.87 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→37.87 Å
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Refine LS restraints |
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LS refinement shell |
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