+Open data
-Basic information
Entry | Database: PDB / ID: 7b9a | ||||||
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Title | CooS-V with Xe-soaked | ||||||
Components | Carbon monoxide dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Hybrid cluster / HCP / CODH | ||||||
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 / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / peroxidase activity / 4 iron, 4 sulfur cluster binding Similarity search - Function | ||||||
Biological species | Carboxydothermus hydrogenoformans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Jeoung, J.H. / Dobbek, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold. Authors: Jeoung, J.H. / Fesseler, J. / Domnik, L. / Klemke, F. / Sinnreich, M. / Teutloff, C. / Dobbek, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b9a.cif.gz | 467.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b9a.ent.gz | 384.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b9a_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 7b9a_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 7b9a_validation.xml.gz | 83.4 KB | Display | |
Data in CIF | 7b9a_validation.cif.gz | 112.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/7b9a ftp://data.pdbj.org/pub/pdb/validation_reports/b9/7b9a | HTTPS FTP |
-Related structure data
Related structure data | 7b7qSC 7b7tC 7b95C 7b97C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 68287.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) (bacteria) Strain: ATCC BAA-161 / DSM 6008 / Z-2901 / Gene: cooSV, CHY_0034 / Production host: Escherichia coli (E. coli) References: UniProt: Q3AG28, anaerobic carbon monoxide dehydrogenase |
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-Non-polymers , 6 types, 97 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-XE / #4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-T2N / #6: Chemical | #7: Chemical | |
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-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: 2.37 Å3/Da / Density % sol: 48.09 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris propane (pH 6.5), 0.15 M KSCN and 16-20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.9 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 83046 / % possible obs: 91.6 % / Redundancy: 3.8 % / CC1/2: 0.952 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 34051 / CC1/2: 0.929 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7B7Q Resolution: 2.5→20 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.03 / 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: 196.28 Å2 / Biso mean: 26.6662 Å2 / Biso min: 5.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→20 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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