+Open data
-Basic information
Entry | Database: PDB / ID: 5jlc | |||||||||
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Title | Structure of CYP51 from the pathogen Candida glabrata | |||||||||
Components | Lanosterol 14-alpha demethylase | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCATSE INHIBITOR / pathogen / Candida glabrata / CYP51 / itraconazole / OXIDOREDUCTASE-OXIDOREDUCATSE INHIBITOR complex | |||||||||
Function / homology | Function and homology information sterol 14alpha-demethylase / sterol 14-demethylase activity / cortical endoplasmic reticulum / perinuclear endoplasmic reticulum / ergosterol biosynthetic process / iron ion binding / heme binding / membrane Similarity search - Function | |||||||||
Biological species | Candida glabrata (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | |||||||||
Authors | Keniya, M.V. / Sabherwal, M. / Wilson, R.K. / Sagatova, A.A. / Tyndall, J.D.A. / Monk, B.C. | |||||||||
Funding support | New Zealand, 2items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2018 Title: Crystal Structures of Full-Length Lanosterol 14 alpha-Demethylases of Prominent Fungal Pathogens Candida albicans and Candida glabrata Provide Tools for Antifungal Discovery. Authors: Keniya, M.V. / Sabherwal, M. / Wilson, R.K. / Woods, M.A. / Sagatova, A.A. / Tyndall, J.D.A. / 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. #2: 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 | 5jlc.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jlc.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 5jlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jlc_validation.pdf.gz | 984.1 KB | Display | wwPDB validaton report |
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Full document | 5jlc_full_validation.pdf.gz | 988 KB | Display | |
Data in XML | 5jlc_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 5jlc_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/5jlc ftp://data.pdbj.org/pub/pdb/validation_reports/jl/5jlc | HTTPS FTP |
-Related structure data
Related structure data | 5v5zC 4lxjS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59327.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus) Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65 Gene: ERG11, CYP51, CAGL0E04334g / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ADdelta / References: UniProt: P50859, sterol 14alpha-demethylase |
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-Non-polymers , 6 types, 91 molecules
#2: Chemical | ChemComp-HEM / | ||
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#3: Chemical | ChemComp-1YN / | ||
#4: Chemical | ChemComp-PGE / | ||
#5: Chemical | ChemComp-1PE / | ||
#6: Chemical | #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: 4.73 Å3/Da / Density % sol: 74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.5 M Glycine,40% PEG400 |
-Data collection
Diffraction | Mean temperature: 93 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, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.4→97.14 Å / Num. obs: 44748 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 43.44 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.166 / Net I/σ(I): 7.4 | |||||||||||||||
Reflection shell |
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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: 2.4→48.569 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 24.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.18 Å2 / Biso mean: 47.9072 Å2 / Biso min: 24.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→48.569 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: 30
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