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Yorodumi- PDB-5eah: Saccharomyces cerevisiae CYP51 complexed with the plant pathogen ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eah | ||||||
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Title | Saccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor Difenoconazole | ||||||
Components | Lanosterol 14-alpha demethylase | ||||||
Keywords | Oxidoreductase/Oxidoreducatse inhibitor / CYP51 / Difenoconazole / oxidoreductase-oxidoreductase inhibitor complex / racemic mixture / Oxidoreductase-Oxidoreducatse 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 / molecular replacement / Resolution: 2.541 Å | ||||||
Authors | Tyndall, J.D.A. / Sabherwal, M. / Keniya, M.V. / Wilson, R.K. / Woods, M.V. / Monk, B.C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: PLoS ONE / Year: 2016 Title: Structural and Functional Elucidation of Yeast Lanosterol 14 alpha-Demethylase in Complex with Agrochemical Antifungals. Authors: Tyndall, J.D. / Sabherwal, M. / Sagatova, A.A. / Keniya, M.V. / Negroni, J. / Wilson, R.K. / Woods, M.A. / Tietjen, K. / Monk, B.C. #1: Journal: Antimicrob. Agents Chemother. / Year: 2015 Title: Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14alpha-Demethylase. Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Monk, B.C. / Tyndall, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eah.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eah.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 5eah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eah_validation.pdf.gz | 773.5 KB | Display | wwPDB validaton report |
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Full document | 5eah_full_validation.pdf.gz | 780.9 KB | Display | |
Data in XML | 5eah_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 5eah_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/5eah ftp://data.pdbj.org/pub/pdb/validation_reports/ea/5eah | HTTPS FTP |
-Related structure data
Related structure data | 5eabC 5eacC 5eadC 5eaeC 5eafC 5eagC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61885.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZSR0 |
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-Non-polymers , 6 types, 42 molecules
#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-5LZ / |
#4: Chemical | ChemComp-5LW / |
#5: Chemical | ChemComp-5LX / |
#6: Chemical | ChemComp-5LY / |
#7: 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: 3.46 Å3/Da / Density % sol: 64.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.45 / Details: 45% PEG 400, 0.1M GLYCINE / PH range: 9.4-9.6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.54→79.99 Å / Num. obs: 27403 / % possible obs: 99.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 47.75 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.078 / Net I/σ(I): 6.6 / Num. measured all: 86668 / Scaling rejects: 909 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LXJ Resolution: 2.541→79.99 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 26.62 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.6 Å2 / Biso mean: 60.5627 Å2 / Biso min: 22.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.541→79.99 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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