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Yorodumi- PDB-2q9f: Crystal structure of human cytochrome P450 46A1 in complex with c... -
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-Basic information
Entry | Database: PDB / ID: 2q9f | ||||||
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Title | Crystal structure of human cytochrome P450 46A1 in complex with cholesterol-3-sulphate | ||||||
Components | Cytochrome P450 46A1 | ||||||
Keywords | OXIDOREDUCTASE / CYP46A1 / P450 46A1 / P450 / MONOOXYGENASE / CHOLESTEROL METABOLIC ENZYME / HEME / cholesterol-3-sulphate | ||||||
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 / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å | ||||||
Authors | White, M.A. / Mast, N.V. / Johnson, E.F. / Stout, C.D. / Pikuleva, I.A. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1. Authors: White, M.A. / Mast, N. / 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 | 2q9f.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q9f.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 2q9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q9f_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2q9f_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2q9f_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 2q9f_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/2q9f ftp://data.pdbj.org/pub/pdb/validation_reports/q9/2q9f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52125.086 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP46A1, CYP46 / Plasmid: PUC18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q9Y6A2, EC: 1.14.13.98 |
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-Non-polymers , 5 types, 139 molecules
#2: Chemical | ChemComp-PO4 / | ||
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#3: Chemical | ChemComp-HEM / | ||
#4: Chemical | ChemComp-C3S / | ||
#5: Chemical | ChemComp-GOL / #6: 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: 2.4 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: PEG8000, Potassium Phosphate, Glycerol, NaCl, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, pH 4.6, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 / Wavelength: 0.97945 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2007 Details: FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HO RIZONTAL FOCUSING) |
Radiation | Monochromator: SIDE SCATTERING BENT CUBE- ROOT I-BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.68 Å / Num. all: 42756 / Num. obs: 42756 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.97 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.9→43.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4155867.19 / Data cutoff low absF: 0 / Isotropic thermal model: variable / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Refmac5 and TLS used in intermediate refinement steps. TLS not used in CNS refinement. TLS groups determined using the TLSMD server. TLSMD REF: J Painter & E A Merritt (2006) J. Appl. Cryst. ...Details: Refmac5 and TLS used in intermediate refinement steps. TLS not used in CNS refinement. TLS groups determined using the TLSMD server. TLSMD REF: J Painter & E A Merritt (2006) J. Appl. Cryst. 39, 109-111. PMB used in all CNS refinements: PMB BOND target set to 0.020, PMB Variable Sigma-B used default parameters. PMB Hydrogen bond restraints not used. PMB Local scale reject set to 30 sigma, PMB Local Scale rejected 213 reflections of 42738, PMB Local Scale rejected reflections test flag+=90. PMB Local Scale (h,k,l) box sizes = +/- 4 3 5, PMB Local Scale maximum scale used (localscale method): 15.179, PMB Local Scale minimum scale used (localscale method): 6.502
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.8114 Å2 / ksol: 0.360044 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→43.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.93 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 20
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Xplor file |
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