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Yorodumi- PDB-1n61: Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Dithionit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n61 | ||||||
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Title | Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Dithionite reduced state | ||||||
Components | (Carbon monoxide dehydrogenase ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / CODH / molybdenum / molybdopterin | ||||||
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: 1.3 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 | 1n61.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1n61.ent.gz | 887.1 KB | Display | PDB format |
PDBx/mmJSON format | 1n61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n61_validation.pdf.gz | 704 KB | Display | wwPDB validaton report |
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Full document | 1n61_full_validation.pdf.gz | 748.9 KB | Display | |
Data in XML | 1n61_validation.xml.gz | 53.7 KB | Display | |
Data in CIF | 1n61_validation.cif.gz | 97.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/1n61 ftp://data.pdbj.org/pub/pdb/validation_reports/n6/1n61 | 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, 3006 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: 2.29 Å3/Da / Density % sol: 46.28 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: sodium, potassium phosphate, MPD, HEPES, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K | |||||||||||||||||||||||||||||||||||
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 source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.06 Å |
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Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→17 Å / Num. all: 632876 / Num. obs: 632876 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.28→1.32 Å / % possible all: 97.6 |
Reflection | *PLUS Highest resolution: 1.28 Å / Lowest resolution: 17 Å / Num. measured all: 2011470 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→17 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.3→17 Å
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Refinement | *PLUS Lowest resolution: 17 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.148 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19 |