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- PDB-8x9e: Crystal structure of CO dehydrogenase mutant with increased affin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8x9e | ||||||
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Title | Crystal structure of CO dehydrogenase mutant with increased affinity for electron mediators in low PEG concentration | ||||||
![]() | Carbon monoxide dehydrogenase 2 | ||||||
![]() | ELECTRON TRANSPORT / OXIDOREDUCTASE | ||||||
Function / homology | ![]() anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / response to hydrogen peroxide / peroxidase activity / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, H.H. / Heo, Y. / Yoon, H.J. / Kim, S.M. / Kong, S.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity. Authors: Kim, S.M. / Kang, S.H. / Lee, J. / Heo, Y. / Poloniataki, E.G. / Kang, J. / Yoon, H.J. / Kong, S.Y. / Yun, Y. / Kim, H. / Ryu, J. / Lee, H.H. / Kim, Y.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 | ![]() | 248.8 KB | Display | ![]() |
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PDB format | ![]() | 196.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.6 KB | Display | ![]() |
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Full document | ![]() | 492.5 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8x9dC ![]() 8x9fC ![]() 8x9gC ![]() 8x9hC 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 69062.789 Da / Num. of mol.: 1 / Mutation: R57G, N59L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cooS2 / Production host: ![]() ![]() References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase |
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-Non-polymers , 6 types, 124 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/XCC.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/XCC.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-FES / |
#4: Chemical | ChemComp-XCC / |
#5: Chemical | ChemComp-FE / |
#6: Chemical | ChemComp-EDO / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.92 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES/NaOH pH 7.5, 200 mM MgCl2, and 25% (w/v) PEG 3,350. |
-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: Dec 20, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 18938 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.058 / Rrim(I) all: 0.115 / Χ2: 0.443 / Net I/σ(I): 4.3 / Num. measured all: 71132 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.5→35.22 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.9508 Å / Origin y: -0.7721 Å / Origin z: 14.503 Å
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Refinement TLS group | Selection details: all |