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Yorodumi- PDB-3vm4: Cytochrome P450SP alpha (CYP152B1) in complex with (R)-ibuprophen -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vm4 | ||||||
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Title | Cytochrome P450SP alpha (CYP152B1) in complex with (R)-ibuprophen | ||||||
Components | Fatty acid alpha-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Sphingomonas paucimobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||
Authors | Fujishiro, T. / Shoji, O. / Nagano, S. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. | ||||||
Citation | Journal: Chem Asian J / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vm4.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vm4.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 3vm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vm4_validation.pdf.gz | 811.7 KB | Display | wwPDB validaton report |
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Full document | 3vm4_full_validation.pdf.gz | 813.1 KB | Display | |
Data in XML | 3vm4_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3vm4_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/3vm4 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/3vm4 | HTTPS FTP |
-Related structure data
Related structure data | 3awmS 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: 45625.848 Da / Num. of mol.: 1 / Fragment: Residues 9-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Plasmid: pGEX-AX2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O24782, fatty-acid peroxygenase | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-IZP / ( | ||
#4: Chemical | #5: 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: 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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