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Yorodumi- PDB-5tz1: Crystal structure of sterol 14-alpha demethylase (CYP51) from Can... -
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-Basic information
Entry | Database: PDB / ID: 5tz1 | ||||||
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Title | Crystal structure of sterol 14-alpha demethylase (CYP51) from Candida albicans in complex with the tetrazole-based antifungal drug candidate VT1161 (VT1) | ||||||
Components | Sterol 14-alpha demethylase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / CYP51 / cytochrome P450 / heme / oxidoreductase / monooxygenase / sterol biosynthesis / eukaryotic membranes / cytochrome P450 fold / endoplasmic reticulum membrane / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information cell growth mode switching, budding to filamentous / membrane raft polarization / sterol 14alpha-demethylase / sterol 14-demethylase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / endosome organization / ergosterol biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity ...cell growth mode switching, budding to filamentous / membrane raft polarization / sterol 14alpha-demethylase / sterol 14-demethylase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / endosome organization / ergosterol biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / methyltransferase activity / lipid metabolic process / methylation / oxidoreductase activity / iron ion binding / endoplasmic reticulum membrane / heme binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hargrove, T. / Wawrzak, Z. / Lepesheva, G. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural analyses of Candida albicans sterol 14 alpha-demethylase complexed with azole drugs address the molecular basis of azole-mediated inhibition of fungal sterol biosynthesis. Authors: Hargrove, T.Y. / Friggeri, L. / Wawrzak, Z. / Qi, A. / Hoekstra, W.J. / Schotzinger, R.J. / York, J.D. / Guengerich, F.P. / Lepesheva, G.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tz1.cif.gz | 217 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tz1.ent.gz | 173.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/5tz1 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/5tz1 | HTTPS FTP |
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-Related structure data
Related structure data | 5fsaSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56435.188 Da / Num. of mol.: 2 / Mutation: A48P, S263L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: CYP51, ERG11 / Variant: 1 / Plasmid: pCW / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): HMS-174 References: UniProt: Q9P4W0, UniProt: P10613*PLUS, sterol 14alpha-demethylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M HEPES, pH 7.4, 0.2 M sodium chloride, 10% PEG6000, 0.03 mM n-Tridecyl-b-D-maltoside |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97849 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2016 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.61 Å / Num. obs: 65813 / % possible obs: 98.8 % / Redundancy: 5 % / CC1/2: 0.943 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2 / % possible all: 96.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5FSA Resolution: 2→49.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.117 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.168 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.745 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.61 Å
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Refine LS restraints |
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