[English] 日本語
Yorodumi- PDB-5e0e: Crystal Structure of Cytochrome P450 2B37 from Desert Woodrat in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e0e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Cytochrome P450 2B37 from Desert Woodrat in complex with 4-(4-chlorophenyl)imidazole | ||||||
Components | Cytochrome P450 family 2 subfamily B | ||||||
Keywords | Oxidoreductase/Oxidoreductase inhibitor / Cytochrome P450 / CYP2B37 / 4-(4-chlorophenyl)imidazole / Inhibitor / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information unspecific monooxygenase / aromatase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Neotoma lepida (desert woodrat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Shah, M.B. / Halpert, J.R. / Stout, C.D. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2016 Title: Structure-Function Analysis of Mammalian CYP2B Enzymes Using 7-Substituted Coumarin Derivatives as Probes: Utility of Crystal Structures and Molecular Modeling in Understanding Xenobiotic Metabolism. Authors: Shah, M.B. / Liu, J. / Huo, L. / Zhang, Q. / Dearing, M.D. / Wilderman, P.R. / Szklarz, G.D. / Stout, C.D. / Halpert, J.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5e0e.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5e0e.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 5e0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/5e0e ftp://data.pdbj.org/pub/pdb/validation_reports/e0/5e0e | HTTPS FTP |
---|
-Related structure data
Related structure data | 5e58C 1suoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53198.863 Da / Num. of mol.: 1 / Fragment: UNP residues 29-491 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neotoma lepida (desert woodrat) / Gene: CYP2B / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: J9JD75 | ||
---|---|---|---|
#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.73 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris and 45% Polypropylene Glycol P400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→42.36 Å / Num. obs: 14619 / % possible obs: 97.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 3.4→3.48 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.6 / % possible all: 91.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SUO Resolution: 3.4→42.36 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.887 / SU B: 24.99 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 86.27 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→42.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|