+Open data
-Basic information
Entry | Database: PDB / ID: 5iuz | ||||||
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Title | STRUCTURE OF P450 2B4 F202W MUTANT (CYMAL-5) | ||||||
Components | Cytochrome P450 2B4 | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / MEMBRANE PROTEIN | ||||||
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: 2.73 Å | ||||||
Authors | Jang, H.-H. / Halpert, J.R. / Shah, M.B. | ||||||
Citation | Journal: Biophys.Chem. / Year: 2016 Title: Effect of detergent binding on cytochrome P450 2B4 structure as analyzed by X-ray crystallography and deuterium-exchange mass spectrometry. Authors: Shah, M.B. / Jang, H.H. / Wilderman, P.R. / Lee, D. / Li, S. / Zhang, Q. / 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 | 5iuz.cif.gz | 208.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iuz.ent.gz | 164 KB | Display | PDB format |
PDBx/mmJSON format | 5iuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iuz_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5iuz_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5iuz_validation.xml.gz | 39.9 KB | Display | |
Data in CIF | 5iuz_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/5iuz ftp://data.pdbj.org/pub/pdb/validation_reports/iu/5iuz | HTTPS FTP |
-Related structure data
Related structure data | 5iutC 3mvrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 54484.406 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-491 / Mutation: F202W, P221S, H226Y Source method: isolated from a genetically manipulated source 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 / | Sequence details | AUTHORS INDICATE THAT THERE IS AN ERROR IN THE SEQUENCE DATABASE REFERENCE AT RESIDUE 221 | |
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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: 3.37 Å3/Da / Density % sol: 63.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5% V/V TACSIMATE, PH 7.0, 0.1 M HEPES, PH 7.0, 10% V/V PEG5000 MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013 |
Radiation | Monochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→54.6 Å / Num. obs: 37793 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 5.95 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.72→2.79 Å / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.1 / % possible all: 25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MVR Resolution: 2.73→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.671 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.534 / ESU R Free: 0.354 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.73→20 Å
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Refine LS restraints |
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