+Open data
-Basic information
Entry | Database: PDB / ID: 6ay6 | ||||||
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Title | Naegleria fowleri CYP51-voriconazole complex | ||||||
Components | CYP51, sterol 14alpha-demethylase | ||||||
Keywords | OXIDOREDUCTASE / CYP51 / sterol 14alpha-demethylase | ||||||
Function / homology | Function and homology information steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Naegleria fowleri (brain-eating amoeba) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Debnath, A. / Calvet, C.M. / Jennings, G. / Zhou, W. / Aksenov, A. / Luth, M. / Abagyan, R. / Nes, W.D. / McKerrow, J.H. / Podust, L.M. | ||||||
Citation | Journal: PLoS Negl Trop Dis / Year: 2017 Title: CYP51 is an essential drug target for the treatment of primary amoebic meningoencephalitis (PAM). Authors: Debnath, A. / Calvet, C.M. / Jennings, G. / Zhou, W. / Aksenov, A. / Luth, M.R. / Abagyan, R. / Nes, W.D. / McKerrow, J.H. / Podust, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ay6.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ay6.ent.gz | 156.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ay6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ay6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ay6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ay6_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 6ay6_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ay6 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ay6 | HTTPS FTP |
-Related structure data
Related structure data | 6ay4C 6aybC 6aycC 5tl8S 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
#1: Protein | Mass: 53575.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Coding sequence synthetically generated Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba) Gene: NF0102700 / Plasmid: pCW-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: A0A2H4A2U9*PLUS |
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#2: Chemical | ChemComp-VOR / |
#3: Chemical | ChemComp-HEM / |
#4: 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: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 33% PEG MME 550, 0.03 M CaCl2, 2% Jeffamine, 0.1 M bis-Tris propane, pH 7.1 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 110 K / Ambient temp details: Nitrogen stream |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2017 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→71.92 Å / Num. obs: 18189 / % possible obs: 97.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.01 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 0.47 / Num. unique obs: 914 / % possible all: 66.5 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.462
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TL8 Resolution: 2.4→71.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 24.067 / SU ML: 0.282 / SU R Cruickshank DPI: 0.6381 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.638 / ESU R Free: 0.33 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.6 Å2 / Biso mean: 85.259 Å2 / Biso min: 39.52 Å2
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Refinement step | Cycle: final / Resolution: 2.4→71.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.402→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.4357 Å / Origin y: -0.1883 Å / Origin z: 19.1498 Å
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