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- PDB-5b2y: Crystal Structure of P450BM3 with N-perfluorodecanoyl-L-tryptophan -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b2y | ||||||||||||
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Title | Crystal Structure of P450BM3 with N-perfluorodecanoyl-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 | ![]() | 209.5 KB | Display | ![]() |
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PDB format | ![]() | 165.2 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 | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 57.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b2uC ![]() 5b2vC ![]() 5b2wC ![]() 5b2xC ![]() 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: 52300.660 Da / Num. of mol.: 2 / Fragment: UNP Residues1-456 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.49 % / Mosaicity: 1.448 ° / Mosaicity esd: 0.003 ° |
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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-perfluorodecanoyl-L-tryptophan, 0.5% (v/v) dimethyl sulfoxide, 105mM MgCl, 10.5% (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: Jan 27, 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: 2→50 Å / Num. obs: 69252 / % possible obs: 98.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.036 / Rrim(I) all: 0.066 / Χ2: 1.019 / Net I/av σ(I): 20.039 / Net I/σ(I): 13.2 / Num. measured all: 221969 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WSP Resolution: 2.01→19.76 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.738 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1836 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.158 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: 95.77 Å2 / Biso mean: 27.766 Å2 / Biso min: 10.69 Å2
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Refinement step | Cycle: final / Resolution: 2.01→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.007→2.059 Å / Total num. of bins used: 20
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