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Yorodumi- PDB-6c94: Structure Of Cytochrome P450 4B1 (CYP4B1) Complexed with the Inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c94 | ||||||
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Title | Structure Of Cytochrome P450 4B1 (CYP4B1) Complexed with the Inhibitor HET0016 | ||||||
Components | Cytochrome P450 4B1 | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / cytochrome P450 / fatty acid omega-hydroxylase / cyp4b1 / inhibitor / HET0016 / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information unspecific monooxygenase / aromatase activity / iron ion binding / endoplasmic reticulum membrane / heme binding Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Hsu, M.-H. / Johnson, E.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Noncovalent interactions dominate dynamic heme distortion in cytochrome P450 4B1. Authors: Jennings, G.K. / Hsu, M.H. / Shock, L.S. / Johnson, E.F. / Hackett, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c94.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c94.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 6c94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c94_validation.pdf.gz | 827.5 KB | Display | wwPDB validaton report |
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Full document | 6c94_full_validation.pdf.gz | 831.2 KB | Display | |
Data in XML | 6c94_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 6c94_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/6c94 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/6c94 | HTTPS FTP |
-Related structure data
Related structure data | 6c93C 5t6qS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57847.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP4B1 / Production host: Escherichia coli (E. coli) / Strain (production host): dH5alpha / References: UniProt: P15128, unspecific monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-V16 / |
#4: 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: 3.82 Å3/Da / Density % sol: 67.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→38.59 Å / Num. obs: 24218 / % possible obs: 99.8 % / Redundancy: 10.2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.086 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.72→2.85 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3145 / CC1/2: 0.856 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T6Q Resolution: 2.72→38.59 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / Phase error: 23.46 Details: The DivCon 6 plugin for Phenix was used for stereo-chemical restraints for the covalently bound HEM-GLU310 ester during refinement The longer than expected E310 CD-OE2 bond length is ...Details: The DivCon 6 plugin for Phenix was used for stereo-chemical restraints for the covalently bound HEM-GLU310 ester during refinement The longer than expected E310 CD-OE2 bond length is consistent with the single bond in the ester linkage to the heme CMD carbon.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→38.59 Å
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Refine LS restraints |
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LS refinement shell |
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