[English] 日本語
Yorodumi- PDB-3l4d: Crystal structure of sterol 14-alpha demethylase (CYP51) from Lei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l4d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of sterol 14-alpha demethylase (CYP51) from Leishmania infantum in complex with fluconazole | ||||||
Components | Sterol 14-alpha demethylase | ||||||
Keywords | OXIDOREDUCTASE / sterol 14-alpha demethylase / CYP51 / P450 / heme / monooxygenase / endoplasmic reticulum / transmembrane protein / sterol biosynthesis / obtusifoliol / lipids / membrane / Iron | ||||||
Function / homology | Function and homology information sterol 14alpha-demethylase / sterol 14-demethylase activity / methyltransferase activity / methylation / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Leishmania infantum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Lepesheva, G.I. / Hargrove, T.Y. / Wawrzak, Z. / Waterman, M.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Substrate Preferences and Catalytic Parameters Determined by Structural Characteristics of Sterol 14{alpha}-Demethylase (CYP51) from Leishmania infantum. Authors: Hargrove, T.Y. / Wawrzak, Z. / Liu, J. / Nes, W.D. / Waterman, M.R. / Lepesheva, G.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3l4d.cif.gz | 360.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3l4d.ent.gz | 295.1 KB | Display | PDB format |
PDBx/mmJSON format | 3l4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l4d_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3l4d_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 3l4d_validation.xml.gz | 77.7 KB | Display | |
Data in CIF | 3l4d_validation.cif.gz | 99.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/3l4d ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l4d | HTTPS FTP |
-Related structure data
Related structure data | 3g1qS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | Authors state that the biological assembly in the membrane is a transmembrane monomer. In the solution the protein is crystallized as a tetramer. |
-Components
#1: Protein | Mass: 51188.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: CYP51, LinJ11.1100 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: A2TEF2, sterol 14alpha-demethylase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-TPF / #4: Chemical | ChemComp-N8E / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: TRIS-HCL, PEG 6000, 3,6,9,12,15-PENTAOXATRICOSAN-1-OL, FLUCONAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2007 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→50 Å / Num. obs: 47888 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 87.7 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.74→2.84 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.82 / Rsym value: 0.558 / % possible all: 92.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3g1q Resolution: 2.75→48.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 47.662 / SU ML: 0.413 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.942 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→48.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.818 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|