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- PDB-5b2u: Crystal Structure of P450BM3 with N-perfluorohexanoyl -L-tryptophan -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b2u | |||||||||
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Title | Crystal Structure of P450BM3 with N-perfluorohexanoyl -L-tryptophan | |||||||||
![]() | Bifunctional cytochrome P450/NADPH--P450 reductase | |||||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Cong, Z. / Shoji, O. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.9 KB | Display | ![]() |
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PDB format | ![]() | 166.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 40.7 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b2vC ![]() 5b2wC ![]() 5b2xC ![]() 5b2yC ![]() 3wspS S: Starting model for refinement C: citing same article ( |
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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: 52376.754 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-456 / Mutation: A328F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % |
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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% (w/v) PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2015 |
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: 1.9→50 Å / Num. obs: 73762 / % possible obs: 90.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 20.52 |
Reflection shell | Resolution: 1.9→1.97 Å |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WSP Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.061 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1605 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.142 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: 73.84 Å2 / Biso mean: 23.925 Å2 / Biso min: 11.75 Å2
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Refinement step | Cycle: final / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.898→1.947 Å / Total num. of bins used: 20
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