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Yorodumi- PDB-4zdy: Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zdy | |||||||||
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Title | Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) Y140F mutant complexed with itraconazole | |||||||||
Components | Lanosterol 14-alpha demethylase | |||||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / Itraconazole / CYP51 / oxidoreductase-oxidoreducatse inhibitor complex / resistance mutation / oxidoreductase-oxidoreductase inhibitor complex | |||||||||
Function / homology | Function and homology information ergosterol biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / methyltransferase activity / methylation / iron ion binding / heme binding / endoplasmic reticulum / membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Sagatova, A. / Keniya, M.V. / Wilson, R.K. / Tyndall, J.D.A. / Monk, B.C. | |||||||||
Funding support | New Zealand, 2items
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Citation | Journal: Sci Rep / Year: 2016 Title: Triazole resistance mediated by mutations of a conserved active site tyrosine in fungal lanosterol 14 alpha-demethylase. Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / Tyndall, J.D. / Monk, B.C. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014 Title: Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer. Authors: Monk, B.C. / Tomasiak, T.M. / Keniya, M.V. / Huschmann, F.U. / Tyndall, J.D. / O'Connell, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zdy.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zdy.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zdy_validation.pdf.gz | 995.5 KB | Display | wwPDB validaton report |
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Full document | 4zdy_full_validation.pdf.gz | 997.8 KB | Display | |
Data in XML | 4zdy_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 4zdy_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/4zdy ftp://data.pdbj.org/pub/pdb/validation_reports/zd/4zdy | HTTPS FTP |
-Related structure data
Related structure data | 4zdzC 4ze0C 4ze1C 4ze2C 4ze3C 5hs1C 4lxjS 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: 61869.215 Da / Num. of mol.: 1 / Mutation: Y140F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast) Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD2Delta / References: UniProt: A6ZSR0 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-1YN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.4 / Details: 45% PEG 400, 0.1 M Glycine / PH range: 9.3 - 9.55 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→34.27 Å / Num. obs: 54071 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.02→2.13 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 3.3 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LXJ Resolution: 2.02→33.37 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→33.37 Å
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Refine LS restraints |
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LS refinement shell |
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