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Yorodumi- PDB-7err: Tunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7err | |||||||||
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Title | Tunnel-redesigned O2-tolerant CO dehydrogenase for removal of CO in real flue gas (Aerobic ChCODH2 A559W mutant) | |||||||||
Components | Carbon monoxide dehydrogenase 2 | |||||||||
Keywords | OXIDOREDUCTASE / Carbon monoxide dehydrogenase / ELECTRON TRANSPORT | |||||||||
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: 2.26 Å | |||||||||
Authors | Heo, Y.Y. / Kim, S.M. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Nat Catal / Year: 2022 Title: O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas Authors: Kim, S.M. / Lee, J.H. / Kang, S.H. / Heo, Y.Y. / Yoon, H.J. / Hahn, J.S. / 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 | 7err.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7err.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 7err.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7err_validation.pdf.gz | 914.5 KB | Display | wwPDB validaton report |
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Full document | 7err_full_validation.pdf.gz | 918.1 KB | Display | |
Data in XML | 7err_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 7err_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/7err ftp://data.pdbj.org/pub/pdb/validation_reports/er/7err | HTTPS FTP |
-Related structure data
Related structure data | 7xdmC 7xdnC 7xdpC 1su7S S: Starting model for refinement 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
#1: Protein | Mass: 69307.023 Da / Num. of mol.: 1 / Mutation: A559W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooS2, cooSII, CHY_0085 / Production host: Escherichia coli (E. coli) References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-FES / |
#4: Chemical | ChemComp-NFS / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES/NaOH pH 7.0, 50 mM MgCl2, 25 % (w/v) polyethyleneglycol 3350 |
-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: Oct 21, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.26→50 Å / Num. obs: 25635 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.26 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.063 / Rrim(I) all: 0.118 / Χ2: 0.681 / Net I/σ(I): 5.5 / Num. measured all: 86418 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SU7 Resolution: 2.26→40.72 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.07 Å2 / Biso mean: 35.9194 Å2 / Biso min: 17.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.26→40.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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