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Yorodumi- PDB-1n5w: Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Oxidized form -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n5w | |||||||||
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Title | Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Oxidized form | |||||||||
Components | (Carbon monoxide dehydrogenase ...) x 3 | |||||||||
Keywords | OXIDOREDUCTASE / molybdopterin / molybdenum / MCD | |||||||||
Function / homology | Function and homology information aerobic carbon monoxide dehydrogenase / carbon-monoxide oxygenase activity / : / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Oligotropha carboxidovorans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Dobbek, H. / Gremer, L. / Kiefersauer, R. / Huber, R. / Meyer, O. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Catalysis at a dinuclear [CuSMo(=O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution Authors: Dobbek, H. / Gremer, L. / Kiefersauer, R. / Huber, R. / Meyer, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n5w.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1n5w.ent.gz | 856.3 KB | Display | PDB format |
PDBx/mmJSON format | 1n5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n5w_validation.pdf.gz | 645.9 KB | Display | wwPDB validaton report |
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Full document | 1n5w_full_validation.pdf.gz | 682.1 KB | Display | |
Data in XML | 1n5w_validation.xml.gz | 52.1 KB | Display | |
Data in CIF | 1n5w_validation.cif.gz | 93.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/1n5w ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n5w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Carbon monoxide dehydrogenase ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 17810.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oligotropha carboxidovorans (bacteria) / Strain: OM5 References: UniProt: P19921, carbon-monoxide dehydrogenase (acceptor) #2: Protein | Mass: 88847.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oligotropha carboxidovorans (bacteria) / Strain: OM5 References: UniProt: P19919, carbon-monoxide dehydrogenase (acceptor) #3: Protein | Mass: 30276.939 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oligotropha carboxidovorans (bacteria) / Strain: OM5 References: UniProt: P19920, carbon-monoxide dehydrogenase (acceptor) |
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-Non-polymers , 6 types, 2490 molecules
#4: Chemical | ChemComp-PO4 / | ||||||||
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#5: Chemical | ChemComp-FES / #6: Chemical | #7: Chemical | #8: Chemical | #9: 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: 2.3 Å3/Da / Density % sol: 46.47 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: sodium, potassium phospate, HEPES, MPD, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: Dobbek, H., (1999) Proc.Natl.Acad.Sci.USA, 96, 8884. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1999 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→20 Å / Num. all: 387014 / Num. obs: 387014 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.49→1.52 Å / % possible all: 65.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 941420 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→18 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→18 Å
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Refinement | *PLUS Lowest resolution: 18 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.169 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.2 / Rfactor Rwork: 0.13 |