+Open data
-Basic information
Entry | Database: PDB / ID: 8x9g | ||||||
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Title | Crystal structure of CO dehydrogenase mutant in complex with BV | ||||||
Components | Carbon monoxide dehydrogenase 2 | ||||||
Keywords | ELECTRON TRANSPORT / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / hydroxylamine reductase 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 | Carboxydothermus hydrogenoformans Z-2901 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å | ||||||
Authors | Lee, H.H. / Heo, Y. / Yoon, H.J. / Kim, S.M. / Kong, S.Y. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nat Commun / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x9g.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x9g.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 8x9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x9g_validation.pdf.gz | 700.5 KB | Display | wwPDB validaton report |
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Full document | 8x9g_full_validation.pdf.gz | 708.6 KB | Display | |
Data in XML | 8x9g_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 8x9g_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/8x9g ftp://data.pdbj.org/pub/pdb/validation_reports/x9/8x9g | HTTPS FTP |
-Related structure data
Related structure data | 8x9dC 8x9eC 8x9fC 8x9hC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Strain: Z-2901 / Gene: cooS2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase |
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-Non-polymers , 6 types, 8 molecules
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-FES / |
#4: Chemical | ChemComp-XCC / |
#5: Chemical | ChemComp-PGE / |
#6: Chemical | ChemComp-S7L / Mass: 338.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N2 / Feature type: SUBJECT OF INVESTIGATION |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.17 % |
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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) polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.1→50 Å / Num. obs: 10065 / % possible obs: 98.8 % / Redundancy: 5.1 % / CC1/2: 0.974 / CC star: 0.993 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.072 / Rrim(I) all: 0.165 / Χ2: 0.904 / Net I/σ(I): 5.7 / Num. measured all: 51029 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→35.32 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.65 / 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: 3.11→35.32 Å
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Refine LS restraints |
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LS refinement shell |
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