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Yorodumi- PDB-3g1q: Crystal structure of sterol 14-alpha demethylase (CYP51) from Try... -
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-Basic information
Entry | Database: PDB / ID: 3g1q | ||||||
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Title | Crystal structure of sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in ligand free state | ||||||
Components | Sterol 14-alpha-demethylase | ||||||
Keywords | OXIDOREDUCTASE / sterol 14-alpha demethylase / CYP51 / cytochrome P450 / heme / monooxygenase / membrane protein / sterol biosynthesis | ||||||
Function / homology | Function and homology information membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol metabolic process / bile acid biosynthetic process / cholesterol homeostasis / nuclear envelope / oxidoreductase activity ...membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol metabolic process / bile acid biosynthetic process / cholesterol homeostasis / nuclear envelope / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / combination of molecular replacement, Fe-SAD / Resolution: 1.89 Å | ||||||
Authors | Lepesheva, G.I. / Hargrove, T.Y. / Harp, J. / Wawrzak, Z. / Waterman, M.R. / Park, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal structures of Trypanosoma brucei sterol 14alpha-demethylase and implications for selective treatment of human infections. Authors: Lepesheva, G.I. / Park, H.W. / Hargrove, T.Y. / Vanhollebeke, B. / Wawrzak, Z. / Harp, J.M. / Sundaramoorthy, M. / Nes, W.D. / Pays, E. / Chaudhuri, M. / Villalta, F. / Waterman, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g1q.cif.gz | 365.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g1q.ent.gz | 298.4 KB | Display | PDB format |
PDBx/mmJSON format | 3g1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/3g1q ftp://data.pdbj.org/pub/pdb/validation_reports/g1/3g1q | HTTPS FTP |
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-Related structure data
Related structure data | 3gw9C 2ve4S 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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Unit cell |
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Details | AUTHORS STATE THIS IS A MEMBRANE BOUND PROTEIN THAT IS FUNCTIONALLY A MONOMER AND FORMS COMPLEX WITH THE ELECTRON DONOR PARTNER CYTOCHROME P450 REDUCTASE. |
-Components
#1: Protein | Mass: 50976.152 Da / Num. of mol.: 4 / Mutation: T27S, R28K, P29G, T30K, D31L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Cellular location: membraneBiological membrane / 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: 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: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: PEG 3350, POTASSIUM PHOSPHATE, n-TETRADECYL-BETA-D-MALTOSIDE, SODIUM CHLORIDE , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.89→30 Å / Num. all: 153658 / Num. obs: 150278 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5 | ||||||||||||||||||
Reflection shell | Resolution: 1.89→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.472 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: combination of molecular replacement, Fe-SAD Starting model: PDB ENTRY 2VE4 Resolution: 1.89→28.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.719 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.147 / 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: 36.415 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→28.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.943 Å / Total num. of bins used: 20
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