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Yorodumi- PDB-3mvr: Crystal Structure of cytochrome P450 2B4-H226Y in a closed confor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mvr | ||||||
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Title | Crystal Structure of cytochrome P450 2B4-H226Y in a closed conformation | ||||||
Components | Cytochrome P450 2B4 | ||||||
Keywords | OXIDOREDUCTASE / Ligand free closed conformation / P450 / Cytochrome P450 2B4 / monooxygenase / membrane protein / CYP 2B4. | ||||||
Function / homology | Function and homology information arachidonic acid epoxygenase activity / epoxygenase P450 pathway / unspecific monooxygenase / aromatase activity / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Shah, M.B. / Stout, C.D. / Halpert, J.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Plasticity of Cytochrome P450 2B4 as Investigated by Hydrogen-Deuterium Exchange Mass Spectrometry and X-ray Crystallography. Authors: Wilderman, P.R. / Shah, M.B. / Liu, T. / Li, S. / Hsu, S. / Roberts, A.G. / Goodlett, D.R. / Zhang, Q. / Woods, V.L. / Stout, C.D. / Halpert, J.R. #1: Journal: J.Biol.Chem. / Year: 2006 Title: Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction. Authors: Zhao, Y. / White, M.A. / Muralidhara, B.K. / Sun, L. / Halpert, J.R. / Stout, C.D. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: An open conformation of mammalian cytochrome P450 2B4 at 1.6 A resolution. Authors: Scott, E.E. / He, Y.A. / Wester, M.R. / White, M.A. / Chin, C.C. / Halpert, J.R. / Johnson, E.F. / Stout, C.D. #3: Journal: Biochemistry / Year: 2007 Title: Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4. Authors: Zhao, Y. / Sun, L. / Muralidhara, B.K. / White, M.A. / Stout, C.D. / Halpert, J.R. #4: Journal: Biochemistry / Year: 2009 Title: Crystal Structures of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-methyl-1H-imidazole: Ligand-Induced Structural Response through Alpha-Helical Repositioning Authors: Gay, S.C. / Sun, L. / Maekawa, K. / Halpert, J.R. / Stout, C.D. #5: Journal: J.Biol.Chem. / Year: 2004 Title: Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9 {angstrom} resolution: Insight into the range of P450 conformations and coordination of redox partner binding. Authors: Scott, E.E. / White, M.A. / He, Y.A. / Johnson, E.F. / Stout, C.D. / Halpert, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mvr.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mvr.ent.gz | 171.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mvr_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3mvr_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3mvr_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 3mvr_validation.cif.gz | 64 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/3mvr ftp://data.pdbj.org/pub/pdb/validation_reports/mv/3mvr | HTTPS FTP |
-Related structure data
Related structure data | 2q6nS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54169.082 Da / Num. of mol.: 2 / Fragment: CYP2B4dH Mutation: E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, H226Y Source method: isolated from a genetically manipulated source Details: Deleted residues 3-21, E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, 4 x Cterm His tag Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2B4 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P00178, unspecific monooxygenase #2: Chemical | #3: Chemical | ChemComp-CM5 / #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: 3.35 Å3/Da / Density % sol: 63.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14.4 % (w/v) PEG 8000, 0.08M cacodylate pH 6.5, 0.6M calcium acetate, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→150 Å / Num. all: 138705 / Num. obs: 135654 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 26.276 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.764→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.34 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q6N Resolution: 1.76→150 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.186 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 26.276 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→150 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.764→1.81 Å / Total num. of bins used: 20
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