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Yorodumi- PDB-3p99: Sterol 14alpha-demethylase (CYP51) from Trypanosoma brucei in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p99 | ||||||
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Title | Sterol 14alpha-demethylase (CYP51) from Trypanosoma brucei in complex with delta7-14alpha-methylene-cyclopropyl-dihydrolanosterol | ||||||
Components | Sterol 14-alpha-demethylase | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 fold/sterol 14-alpha demethylase / CYP51 / monooxygenase / hemoprotein / sterol biosynthesis / cytochrome P450 reductase (CPR) / endoplasmic reticulum / membrane | ||||||
Function / homology | Function and homology information membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol metabolic process / nuclear envelope / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Lepesheva, G.I. / Hargrove, T.Y. / Waterman, M.R. / Wawrzak, Z. | ||||||
Citation | Journal: J.Lipid Res. / Year: 2012 Title: Structural complex of sterol 14alpha-demethylase (CYP51) with 14alpha-methylenecyclopropyl-delta7-24, 25-dihydrolanosterol Authors: Hargrove, T.Y. / Wawrzak, Z. / Liu, J. / Waterman, M.R. / Nes, W.D. / Lepesheva, G.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p99.cif.gz | 734.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p99.ent.gz | 615.8 KB | Display | PDB format |
PDBx/mmJSON format | 3p99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p99_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 3p99_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 3p99_validation.xml.gz | 83.9 KB | Display | |
Data in CIF | 3p99_validation.cif.gz | 107 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/3p99 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p99 | HTTPS FTP |
-Related structure data
Related structure data | 3g1qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 51173.395 Da / Num. of mol.: 4 / Fragment: unp residues 29-481 / Mutation: G29P, K30T, L31D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: CYP51, Tb11.02.4080 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q385E8, sterol 14alpha-demethylase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-LNP / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow | Temperature: 297 K / pH: 7.2 Details: PEG 3350, POTASSIUM PHOSPHATE; n-TETRADECYL-BETA-D-MALTOSIDE, SODIUM CHLORIDE, delta7-14alpha-methylene-cyclopropyl-dihydrolanosterol, pH 7.2, VAPOR DIFFUSION, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010 / Details: BE LENSES/DIAMOND LAUE MONO |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 3→29.39 Å / Num. obs: 37941 / % possible obs: 97.6 % / Observed criterion σ(I): 2.6 / Redundancy: 3.8 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.068 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 3.94 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.55 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G1Q Resolution: 3→29.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 51.98 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 84.529 Å2
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Refinement step | Cycle: LAST / Resolution: 3→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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