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Yorodumi- PDB-4udy: NCO- bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4udy | ||||||
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Title | NCO- bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic resolution | ||||||
Components | CARBON MONOXIDE DEHYDROGENASE 2 | ||||||
Keywords | OXIDOREDUCTASE / NCO / NI / FE / CODH | ||||||
Function / homology | Function and homology information anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Fesseler, J. / Jeoung, J.-H. / Dobbek, H. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: How the [Nife4 S4 ] Cluster of Co Dehydrogenase Activates Co2 and Nco(.) Authors: Fesseler, J. / Jeoung, J.H. / Dobbek, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4udy.cif.gz | 384.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4udy.ent.gz | 319.9 KB | Display | PDB format |
PDBx/mmJSON format | 4udy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/4udy ftp://data.pdbj.org/pub/pdb/validation_reports/ud/4udy | HTTPS FTP |
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-Related structure data
-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: 66992.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q9F8A8, carbon-monoxide dehydrogenase (acceptor) |
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-Non-polymers , 6 types, 763 molecules
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-FES / |
#4: Chemical | ChemComp-WCC / |
#5: Chemical | ChemComp-FE2 / |
#6: Chemical | ChemComp-0NM / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % / Description: NONE |
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Crystal grow | pH: 8 / Details: pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 12, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→40.8 Å / Num. obs: 223489 / % possible obs: 98 % / Redundancy: 3.69 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.09→1.13 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.77 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→33.16 Å / Num. parameters: 50098 / Num. restraintsaints: 62069 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 28 / Occupancy sum hydrogen: 4750 / Occupancy sum non hydrogen: 5408.3 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→33.16 Å
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Refine LS restraints |
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