+Open data
-Basic information
Entry | Database: PDB / ID: 1po5 | ||||||
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Title | Structure of mammalian cytochrome P450 2B4 | ||||||
Components | Cytochrome P450 2B4 | ||||||
Keywords | OXIDOREDUCTASE / membrane protein / cyp 2B4 / cyp LM2 / cytochrome P450 / monooxygenase | ||||||
Function / homology | Function and homology information response to stimulus / unspecific monooxygenase / aromatase activity / iron ion binding / heme binding / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
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. | ||||||
Citation | 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. #1: Journal: Arch.Biochem.Biophys. / Year: 2001 Title: A truncation of 2B subfamily cytochromes P450 yields increased expression levels, increased solubility, and decreased aggregation while retaining function Authors: Scott, E.E. / Spatzenegger, M. / Halpert, J.R. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS INFORMED THAT THE GENBANK SEQUENCE IS THOUGHT TO CONTAIN A SEQUENCING ERROR AT RESIDUE 221. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1po5.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1po5.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 1po5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/1po5 ftp://data.pdbj.org/pub/pdb/validation_reports/po/1po5 | HTTPS FTP |
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-Related structure data
Related structure data | 1n6bS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 54144.055 Da / Num. of mol.: 1 Mutation: E2A, G22K, H23K, P24T, K25S, A26S, H27K, R29K, P221S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: 2B4 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P00178, unspecific monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: ethanol, sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2002 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→21.7 Å / Num. obs: 57717 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.591 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 197894 |
Reflection shell | *PLUS % possible obs: 98.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N6B WITH NON-IDENTICAL RESIDUES TRUNCATED AT C-BETA Resolution: 1.6→21.7 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→21.7 Å
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.217 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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