+Open data
-Basic information
Entry | Database: PDB / ID: 3mdm | ||||||
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Title | Thioperamide complex of Cytochrome P450 46A1 | ||||||
Components | Cholesterol 24-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / CYP46A1 / P450 46A1 / P450 / THIOPERAMIDE / MONOOXYGENASE / METABOLIC ENZYME / HEME / Cholesterol metabolism / Endoplasmic reticulum / Iron / Lipid metabolism / Membrane / Metal-binding / Microsome / NADP / Steroid metabolism / Transmembrane | ||||||
Function / homology | Function and homology information cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / bile acid biosynthetic process / regulation of long-term synaptic potentiation / steroid hydroxylase activity ...cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / bile acid biosynthetic process / regulation of long-term synaptic potentiation / steroid hydroxylase activity / Endogenous sterols / cholesterol catabolic process / xenobiotic metabolic process / presynapse / nervous system development / postsynapse / iron ion binding / dendrite / endoplasmic reticulum membrane / heme binding / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Mast, N. / Charvet, C. / Pikuleva, I. / Stout, C.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural basis of drug binding to CYP46A1, an enzyme that controls cholesterol turnover in the brain. Authors: Mast, N. / Charvet, C. / Pikuleva, I.A. / Stout, C.D. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Crystal structures of substrate-bound and substrate-free cytochrome P450 46A1, the principal cholesterol hydroxylase in the brain. Authors: Mast, N. / White, M.A. / Bjorkhem, I. / Johnson, E.F. / Stout, C.D. / Pikuleva, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mdm.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mdm.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 3mdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/3mdm ftp://data.pdbj.org/pub/pdb/validation_reports/md/3mdm | HTTPS FTP |
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-Related structure data
Related structure data | 3mdrC 3mdtC 3mdvC 2q9fS 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: 52125.086 Da / Num. of mol.: 1 / Fragment: UNP residues 51-500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP46, CYP46A1 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q9Y6A2, EC: 1.14.13.98 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-FJZ / |
#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: 2.56 Å3/Da / Density % sol: 51.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 8% PEG 8000, 20% glycerol, 50 mM KPi, pH 5.8, 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: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2009 / Details: Rh coated flat mirror |
Radiation | Monochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→66.242 Å / Num. all: 70320 / Num. obs: 70320 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.6 / Num. unique all: 10140 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q9F Resolution: 1.6→20 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 43.544 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.61 Å2 / Biso mean: 22.297 Å2 / Biso min: 6.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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Xplor file |
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