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- PDB-1io7: THERMOPHILIC CYTOCHROME P450 (CYP119) FROM SULFOLOBUS SOLFATARICU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1io7 | ||||||
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Title | THERMOPHILIC CYTOCHROME P450 (CYP119) FROM SULFOLOBUS SOLFATARICUS: HIGH RESOLUTION STRUCTURAL ORIGIN OF ITS THERMOSTABILITY AND FUNCTIONAL PROPERTIES | ||||||
![]() | CYTOCHROME P450 CYP119 | ||||||
![]() | OXIDOREDUCTASE / Thermophilic / Cytochromo P450 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, S.-Y. / Yamane, K. / Adachi, S. / Shiro, Y. / Sligar, S.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.7 KB | Display | ![]() |
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PDB format | ![]() | 135 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 541.5 KB | Display | ![]() |
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Full document | ![]() | 565.2 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % | ||||||||||||||||||||
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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: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→90 Å / Num. all: 591529 / Num. obs: 122326 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.396 / % possible all: 84.4 |
Reflection | *PLUS Num. measured all: 591529 |
Reflection shell | *PLUS % possible obs: 84.4 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 23.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→80 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 80 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.222 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.332 / Rfactor Rwork: 0.33 |