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Yorodumi- PDB-1io9: THERMOPHILIC CYTOCHROME P450 (CYP119) FROM SULFOLOBUS SOLFATARICU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1io9 | ||||||
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Title | THERMOPHILIC CYTOCHROME P450 (CYP119) FROM SULFOLOBUS SOLFATARICUS: HIGH RESOLUTION STRUCTURAL ORIGIN OF ITS THERMOSTABILITY AND FUNCTIONAL PROPERTIES | ||||||
Components | CYTOCHROME P450 CYP119 | ||||||
Keywords | OXIDOREDUCTASE / Thermophilic / Cytochromo P450 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / lactoperoxidase activity / peroxidase / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Park, S.-Y. / Yamane, K. / Adachi, S. / Shiro, Y. / Sligar, S.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2002 Title: Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties. Authors: Park, S.Y. / Yamane, K. / Adachi, S. / Shiro, Y. / Weiss, K.E. / Maves, S.A. / Sligar, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1io9.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1io9.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 1io9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/1io9 ftp://data.pdbj.org/pub/pdb/validation_reports/io/1io9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42924.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PKWS119 / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.49 Å3/Da / Density % sol: 50.63 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG4000, 0.2M sodium thiocyanate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 48 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 6.4 / Details: Park, S.Y., (2000) Acta Crystallogr., D56, 1173. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. all: 306552 / Num. obs: 51738 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.28 / % possible all: 63.2 |
Reflection | *PLUS Num. measured all: 306552 |
Reflection shell | *PLUS % possible obs: 63.2 % / Rmerge(I) obs: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Native CYP119 Resolution: 2.05→20 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: 40.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.08 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.204 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 40.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.379 / Rfactor Rwork: 0.359 |