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- PDB-3vm4: Cytochrome P450SP alpha (CYP152B1) in complex with (R)-ibuprophen -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vm4 | ||||||
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Title | Cytochrome P450SP alpha (CYP152B1) in complex with (R)-ibuprophen | ||||||
![]() | Fatty acid alpha-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Fujishiro, T. / Shoji, O. / Nagano, S. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. | ||||||
![]() | ![]() Title: Chiral-substrate-assisted stereoselective epoxidation catalyzed by H2O2-dependent cytochrome P450SP alpha Authors: Fujishiro, T. / Shoji, O. / Kawakami, N. / Watanabe, T. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.5 KB | Display | ![]() |
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PDB format | ![]() | 108.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 811.7 KB | Display | ![]() |
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Full document | ![]() | 813.1 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3awmS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45625.848 Da / Num. of mol.: 1 / Fragment: Residues 9-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-IZP / ( | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.33 % / Mosaicity: 0.717 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50mM HEPES, 17.5% MPD, 25mM MES, 10% glycerol, 5mM (R)-ibuprophen, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 24, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→20 Å / Num. obs: 43560 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 27.626 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.143 / Net I/σ(I): 19.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AWM Resolution: 1.94→19.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1888 / WRfactor Rwork: 0.1626 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8943 / SU B: 5.015 / SU ML: 0.067 / SU R Cruickshank DPI: 0.2013 / SU Rfree: 0.1088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.35 Å2 / Biso mean: 19.5151 Å2 / Biso min: 4.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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