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Yorodumi- PDB-1gek: STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gek | ||||||
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Title | STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM | ||||||
Components | CYTOCHROME P450CAM | ||||||
Keywords | OXIDOREDUCTASE / Cytocrome P450cam (Fe-II) / Isocyanide Complexe form | ||||||
Function / homology | Function and homology information camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Lee, D.-S. / Park, S.-Y. / Yamane, K. / Shiro, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structural characterization of n-butyl-isocyanide complexes of cytochromes P450nor and P450cam. Authors: Lee, D.S. / Park, S.Y. / Yamane, K. / Obayashi, E. / Hori, H. / Shiro, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gek.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gek.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/1gek ftp://data.pdbj.org/pub/pdb/validation_reports/ge/1gek | HTTPS FTP |
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-Related structure data
Related structure data | 1geiC 1gejC 1gemC 2cppS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46720.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00183, camphor 5-monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NBN / |
#4: 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: 2.12 Å3/Da / Density % sol: 41.99 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 6 / Details: (NH4)2SO4, pH 6.0, SMALL TUBES, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / pH: 7.4 / Method: unknown / Details: Imai, M., (1989) Proc. Natl. Acad. Sci., 86, 7823. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2000 / Details: mirrors |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. all: 283735 / Num. obs: 40825 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2966 / % possible all: 67.6 |
Reflection shell | *PLUS % possible obs: 67.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CPP Resolution: 1.7→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.023
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.221 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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