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Yorodumi- PDB-8eoh: crystal structure of human Cytochrome P450 8B1 in complex with a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eoh | ||||||
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Title | crystal structure of human Cytochrome P450 8B1 in complex with a C12-Pyridine Containing Steroid | ||||||
Components | 7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / Monooxygenase / sterol 12-hydroxylase | ||||||
Function / homology | Function and homology information 5beta-cholestane-3alpha,7alpha-diol 12alpha-hydroxylase / sterol 12-alpha-hydroxylase activity / 7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity / 5beta-cholestane-3alpha,7alpha-diol 12alpha-hydroxylase activity / Sterols are 12-hydroxylated by CYP8B1 / positive regulation of intestinal cholesterol absorption / Eicosanoids / bile acid signaling pathway / bile acid biosynthetic process / Synthesis of bile acids and bile salts via 24-hydroxycholesterol ...5beta-cholestane-3alpha,7alpha-diol 12alpha-hydroxylase / sterol 12-alpha-hydroxylase activity / 7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity / 5beta-cholestane-3alpha,7alpha-diol 12alpha-hydroxylase activity / Sterols are 12-hydroxylated by CYP8B1 / positive regulation of intestinal cholesterol absorption / Eicosanoids / bile acid signaling pathway / bile acid biosynthetic process / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / sterol metabolic process / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Nicotinamide salvaging / response to cholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to nutrient levels / oxygen binding / iron ion binding / heme binding / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Liu, J. / Scott, E.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Pyridine-containing substrate analogs are restricted from accessing the human cytochrome P450 8B1 active site by tryptophan 281. Authors: Liu, J. / Offei, S.D. / Yoshimoto, F.K. / Scott, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eoh.cif.gz | 192.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eoh.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 8eoh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eoh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8eoh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8eoh_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 8eoh_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/8eoh ftp://data.pdbj.org/pub/pdb/validation_reports/eo/8eoh | HTTPS FTP |
-Related structure data
Related structure data | 7lyxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57129.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP8B1, CYP12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNU6, EC: 1.14.18.8 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-WOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium malonate pH 8.0, 0.1 M Tris pH 8.0, 30% w/v Polyethylene glycol 1,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→39.65 Å / Num. obs: 17297 / % possible obs: 99.2 % / Redundancy: 12.5 % / Biso Wilson estimate: 58.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.054 / Rrim(I) all: 0.194 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.773 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2364 / CC1/2: 0.659 / Rpim(I) all: 0.602 / Rrim(I) all: 1.878 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LYX Resolution: 2.65→39.65 Å / SU ML: 0.3108 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2204 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→39.65 Å
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Refine LS restraints |
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LS refinement shell |
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