+Open data
-Basic information
Entry | Database: PDB / ID: 7zy1 | ||||||
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Title | I567A Mutant of Recombinant CODH-II | ||||||
Components | Carbon monoxide dehydrogenase 2 | ||||||
Keywords | OXIDOREDUCTASE / CLUSTER C / 4FE-4S / CYTOPLASM / IRON / IRON-SULFUR / MEMBRANE / METAL-BINDING / NICKEL / DEHYDROGENASE | ||||||
Function / homology | Function and homology information anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / nickel cation binding / generation of precursor metabolites and energy / 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: 1.434 Å | ||||||
Authors | Basak, Y. / Jeoung, J.H. / Dobbek, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix Authors: Basak, Y. / Jeoung, J.H. / Domnik, L. / Ruickoldt, J. / Dobbek, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zy1.cif.gz | 400.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zy1.ent.gz | 330.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/7zy1 ftp://data.pdbj.org/pub/pdb/validation_reports/zy/7zy1 | HTTPS FTP |
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-Related structure data
Related structure data | 7zx3C 7zx5C 7zx6C 7zxcC 7zxjC 7zxlC 7zxxC 3b51S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 66978.406 Da / Num. of mol.: 1 / Mutation: I567A 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 / Plasmid: PLASMID / Details (production host): PET28A / Production host: Escherichia coli B (bacteria) / Strain (production host): ROSSETTA DE3 References: UniProt: Q9F8A8, anaerobic carbon monoxide dehydrogenase |
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-Non-polymers , 5 types, 820 molecules
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-FES / |
#4: Chemical | ChemComp-WCC / |
#5: Chemical | ChemComp-FE2 / |
#6: 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: 2.11 Å3/Da / Density % sol: 41.64 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, PEG 3350 10-18%, Ammonium sulphate 0.18M |
-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: 0.91841 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→41.01 Å / Num. obs: 100997 / % possible obs: 99.4 % / Redundancy: 3.69 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.43→1.49 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 9818 / CC1/2: 0.707 / Rrim(I) all: 0.633 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B51 Resolution: 1.434→34.24 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.71 / 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: 114.84 Å2 / Biso mean: 23.0375 Å2 / Biso min: 5.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.434→34.24 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 99.7683 Å / Origin y: 12.4188 Å / Origin z: 81.1639 Å
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Refinement TLS group |
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