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Yorodumi- PDB-5b2v: Crystal Structure of P450BM3 with N-perfluorohexanoyl-L-tryptophan -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b2v | ||||||||||||
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Title | Crystal Structure of P450BM3 with N-perfluorohexanoyl-L-tryptophan | ||||||||||||
Components | Bifunctional cytochrome P450/NADPH--P450 reductase | ||||||||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 | ||||||||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Bacillus megaterium (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||||||||
Authors | Cong, Z. / Shoji, O. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: to be published Title: Crystal Structure of P450BM3 with decoy molecules Authors: Cong, Z. / Shoji, O. / Kasai, C. / 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 | 5b2v.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b2v.ent.gz | 156.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/5b2v ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b2v | HTTPS FTP |
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-Related structure data
Related structure data | 5b2uC 5b2wC 5b2xC 5b2yC 3wspS 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: 52300.660 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-456 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1, cyp102 / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | #4: 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: 2.66 Å3/Da / Density % sol: 53.71 % / Mosaicity: 1.223 ° / Mosaicity esd: 0.004 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 75mM Tris-HCl (pH7.9), 50uM N-perfluorohexanoyl L-tryptophan, 0.5% (v/v) dimethyl sulfoxide, 100mM MgCl, 10.0% (w/v) PEG 8000 |
-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: Jul 2, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.3→50 Å / Num. obs: 42832 / % possible obs: 89.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.054 / Net I/av σ(I): 19.022 / Net I/σ(I): 18.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3WSP Resolution: 2.3→19.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.68 / SU ML: 0.184 / SU R Cruickshank DPI: 0.4527 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.268 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.79 Å2 / Biso mean: 46.705 Å2 / Biso min: 21.87 Å2
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Refinement step | Cycle: final / Resolution: 2.3→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.358 Å / Total num. of bins used: 20
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