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Yorodumi- PDB-3juv: Crystal structure of human lanosterol 14alpha-demethylase (CYP51) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3juv | |||||||||
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Title | Crystal structure of human lanosterol 14alpha-demethylase (CYP51) | |||||||||
Components | Lanosterol 14-alpha demethylase | |||||||||
Keywords | OXIDOREDUCTASE / cytochrome p450 / sterol 14alpha-demethylase / Structural Genomics / Structural Genomics Consortium / SGC / Alternative splicing / Cholesterol biosynthesis / Endoplasmic reticulum / Heme / Iron / Lipid synthesis / Membrane / Metal-binding / Microsome / Monooxygenase / NADP / Polymorphism / Steroid biosynthesis / Sterol biosynthesis / Transmembrane | |||||||||
Function / homology | Function and homology information sterol 14-demethylase activity / sterol 14alpha-demethylase / negative regulation of amyloid-beta clearance / sterol metabolic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / steroid biosynthetic process / cholesterol biosynthetic process / negative regulation of protein secretion / Endogenous sterols ...sterol 14-demethylase activity / sterol 14alpha-demethylase / negative regulation of amyloid-beta clearance / sterol metabolic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / steroid biosynthetic process / cholesterol biosynthetic process / negative regulation of protein secretion / Endogenous sterols / Activation of gene expression by SREBF (SREBP) / negative regulation of protein catabolic process / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum membrane / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | |||||||||
Authors | Strushkevich, N. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Usanov, S.A. / Park, H. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: J. Mol. Biol. / Year: 2010 Title: Structural basis of human CYP51 inhibition by antifungal azoles. Authors: Strushkevich, N. / Usanov, S.A. / Park, H.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3juv.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3juv.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 3juv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/3juv ftp://data.pdbj.org/pub/pdb/validation_reports/ju/3juv | HTTPS FTP |
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-Related structure data
Related structure data | 3jusC 3ld6C 3i3k C: citing same article (ref.) S: Starting model for refinement |
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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: 52769.465 Da / Num. of mol.: 1 / Fragment: UNP residues 54-502 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP51, CYP51A1 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q16850, sterol 14alpha-demethylase |
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#2: Polysaccharide | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin / Cyclodextrin |
#3: Chemical | ChemComp-HEM / |
#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: 6.75 Å3/Da / Density % sol: 81.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.5M (NH4)2SO4, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 13, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.12→30 Å / Num. obs: 30272 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 56.363 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.141 / Net I/σ(I): 20.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3I3K 3i3k Resolution: 3.12→24.67 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.825 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.901 Å2
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Refinement step | Cycle: LAST / Resolution: 3.12→24.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.12→3.201 Å / Total num. of bins used: 20
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