+Open data
-Basic information
Entry | Database: PDB / ID: 7rya | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | S. CEREVISIAE CYP51 I471T MUTANT COMPLEXED WITH ITRACONAZOLE | |||||||||
Components | Lanosterol 14-alpha demethylase | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / CYP51 / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX / Sterol Biosynthesis / OXIDOREDUCTASE | |||||||||
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: 2.1 Å | |||||||||
Authors | Graham, D.O. / Wilson, R.K. / Ruma, Y.N. / Keniya, M.V. / Tyndall, J.D. / Monk, B.C. | |||||||||
Funding support | New Zealand, 2items
| |||||||||
Citation | Journal: J Fungi (Basel) / Year: 2021 Title: Structural Insights into the Azole Resistance of the Candida albicans Darlington Strain Using Saccharomyces cerevisiae Lanosterol 14 alpha-Demethylase as a Surrogate. Authors: Graham, D.O. / Wilson, R.K. / Ruma, Y.N. / Keniya, M.V. / Tyndall, J.D.A. / Monk, B.C. #1: 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. #2: Journal: Proc.Natl.Acad.Sci.USA / 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 3rd, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7rya.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7rya.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 7rya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rya_validation.pdf.gz | 1002.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7rya_full_validation.pdf.gz | 1008.5 KB | Display | |
Data in XML | 7rya_validation.xml.gz | 23 KB | Display | |
Data in CIF | 7rya_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/7rya ftp://data.pdbj.org/pub/pdb/validation_reports/ry/7rya | HTTPS FTP |
-Related structure data
Related structure data | 7ry8C 7ry9C 7rybC 4lxjS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 61873.160 Da / Num. of mol.: 1 / Mutation: I471T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast) Strain: YJM789 / Gene: ERG11, SCY_2394 / Variant: SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD2DELTA / References: UniProt: A6ZSR0 |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-1YN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.6 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 44% PEG 400, 0.5 M Glycine, pH 9.5 / PH range: 9.1 - 9.6 |
-Data collection
Diffraction | Mean temperature: 91 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→33.42 Å / Num. obs: 45698 / % possible obs: 95.73 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Net I/σ(I): 13.86 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 4038 / CC1/2: 0.836 / % possible all: 85.33 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LXJ Resolution: 2.1→33.42 Å / SU ML: 0.2908 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 25.9483 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→33.42 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|