+Open data
-Basic information
Entry | Database: PDB / ID: 3vno | ||||||
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Title | Cytochrome P450SP alpha (CYP152B1) mutant R241E | ||||||
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: 2.17 Å | ||||||
Authors | Fujishiro, T. / Shoji, O. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. | ||||||
Citation | Journal: Catalysis Science And Technology / Year: 2016 Title: A substrate-binding-state mimic of H2O2-dependent cytochrome P450 produced by one-point mutagenesis and peroxygenation of non-native substrates Authors: Shoji, O. / Fujishiro, T. / Nishio, K. / Kano, Y. / Kimoto, H. / Chien, S.-C. / Onoda, H. / Muramatsu, A. / Tanaka, S. / Hori, A. / 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 | 3vno.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vno.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vno_validation.pdf.gz | 823.8 KB | Display | wwPDB validaton report |
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Full document | 3vno_full_validation.pdf.gz | 826.6 KB | Display | |
Data in XML | 3vno_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3vno_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vno ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vno | HTTPS FTP |
-Related structure data
Related structure data | 3vooC 3vtjC 3awmS S: Starting model for refinement C: citing same article (ref.) |
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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: 45597.766 Da / Num. of mol.: 1 / Fragment: Residues 9-415 / Mutation: R241E 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-MPD / ( |
#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: 3.2 Å3/Da / Density % sol: 61.53 % / Mosaicity: 0.294 ° |
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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, 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: 2.17→20 Å / Num. obs: 31376 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 42.762 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.095 / Net I/σ(I): 19.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.17→19.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2373 / WRfactor Rwork: 0.2085 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.856 / SU B: 9.696 / SU ML: 0.115 / SU R Cruickshank DPI: 0.2 / SU Rfree: 0.1687 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.169 / 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: 104.19 Å2 / Biso mean: 18.1839 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.226 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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