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Yorodumi- PDB-5eaf: Saccharomyces cerevisiae CYP51 complexed with the plant pathogen ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eaf | ||||||
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Title | Saccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor Fluquinconazole | ||||||
Components | Lanosterol 14-alpha demethylase | ||||||
Keywords | Oxidoreductase/Oxidoreducatse inhibitor / CYP51 / Fluquinconazole / oxidoreductase-oxidoreductase inhibitor complex / 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: 2.65 Å | ||||||
Authors | Tyndall, J.D.A. / Sabherwal, M. / Sagatova, A.A. / 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 | 5eaf.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eaf.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 5eaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eaf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5eaf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5eaf_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 5eaf_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/5eaf ftp://data.pdbj.org/pub/pdb/validation_reports/ea/5eaf | HTTPS FTP |
-Related structure data
Related structure data | 5eabC 5eacC 5eadC 5eaeC 5eagC 5eahC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: HEM / End label comp-ID: HEM
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-Components
#1: Protein | Mass: 61857.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FQC is the small molecule Fluquinconazole Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZSR0 #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: 3.55 Å3/Da / Density % sol: 65.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.6 / 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: Apr 9, 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: 2.65→29.899 Å / Num. obs: 43507 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 47.37 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.065 / Net I/σ(I): 6.8 / Num. measured all: 88236 / Scaling rejects: 37 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.5 % / 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: 2.65→29.899 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.7 / 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: 118.2 Å2 / Biso mean: 59.329 Å2 / Biso min: 26.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→29.899 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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