+Open data
-Basic information
Entry | Database: PDB / ID: 6ayb | ||||||
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Title | Naegleria fowleri CYP51-ketoconazole 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: 1.87 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 | 6ayb.cif.gz | 199.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ayb.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ayb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ayb_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ayb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ayb_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 6ayb_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ayb ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ayb | HTTPS FTP |
-Related structure data
Related structure data | 6ay4C 6ay6C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53591.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CYS 371 and CYS 392 are spontaneously oxidized to sulfenic acid CSO Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba) Plasmid: pCW-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4A2U9*PLUS |
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-Non-polymers , 5 types, 93 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-KKK / | #6: 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: 2.17 Å3/Da / Density % sol: 43.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 33% PEG MME 550, 0.03 CaCl2, 4% Jeffamine M-600, 0.1 M bis-Tris propane, pH 6.9 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: Sep 9, 2016 / Details: MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→70.5 Å / Num. obs: 36286 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 6.07 % / Biso Wilson estimate: 42.85 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.203 / Rrim(I) all: 0.223 / Χ2: 0.698 / Net I/σ(I): 3.79 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TL8 Resolution: 1.87→70.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.777 / SU ML: 0.191 / SU R Cruickshank DPI: 0.2047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.18 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: 91.94 Å2 / Biso mean: 46.123 Å2 / Biso min: 22.81 Å2
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Refinement step | Cycle: final / Resolution: 1.87→70.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.918 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 5.7941 Å / Origin y: 25.6368 Å / Origin z: 89.0848 Å
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