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Yorodumi- PDB-2w09: CYP51 OF M. TUBERCULOSIS BOUND TO AN INHIBITOR CIS-4-METHYL-N-[(1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w09 | ||||||
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Title | CYP51 OF M. TUBERCULOSIS BOUND TO AN INHIBITOR CIS-4-METHYL-N-[(1S)-3-(METHYLSULFANYL)-1-(PYRIDIN-4-YLCARBAMOYL)PROPYL]CYCLOHEXANECARBOXAMIDE | ||||||
Components | CYTOCHROME P450 51 | ||||||
Keywords | OXIDOREDUCTASE / STEROID BIOSYNTHESIS / PROTEIN-INHIBITOR COMPLEX / METAL-BINDING / LIPID SYNTHESIS / NADP / IRON / HEME / CYTOPLASM / MONOOXYGENASE / STEROL BIOSYNTHESIS | ||||||
Function / homology | Function and homology information sterol 14alpha-demethylase (ferredoxin) / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / sterol metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding ...sterol 14alpha-demethylase (ferredoxin) / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / sterol metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Podust, L.M. | ||||||
Citation | Journal: Plos Negl Trop Dis / Year: 2009 Title: Trypanosoma Cruzi Cyp51 Inhibitor Derived from a Mycobacterium Tuberculosis Screen Hit. Authors: Chen, C.-K. / Doyle, P.S. / Yermalitskaya, L.V. / Mackey, Z.B. / Ang, K.K.H. / 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 | 2w09.cif.gz | 196.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w09.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 2w09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w09_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2w09_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2w09_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 2w09_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w09 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w09 | HTTPS FTP |
-Related structure data
Related structure data | 2w0aC 2w0bC 1x8vS C: citing same article (ref.) S: Starting model for refinement |
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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: 51477.285 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: 4XHIS TAG AT THE C-TERMINUS / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: P0A512, UniProt: P9WPP9*PLUS, sterol 14alpha-demethylase | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-CM9 / | ||||
#4: Water | ChemComp-HOH / | ||||
Compound details | ENGINEEREDNonpolymer details | PROTOPORPH | Sequence details | MUTATIONS C37L, C442A ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | Temperature: 296 K / pH: 7.5 Details: 15% PEG 4000, 2% ISOPROPANOL, 0.1 M HEPES, PH=7.5, T=23 C |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 5, 2006 Details: SAGITTAL FOCUSING CRYSTAL AND VERTICALLY FOCUSING DOUBLE MIRROR |
Radiation | Monochromator: SI (220) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→50 Å / Num. obs: 59811 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 45.5 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.4 / % possible all: 79.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X8V Resolution: 1.57→67.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.573 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3, 85-100, 217-222, 235-237, 450- 451 ARE DISORDERED DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→67.57 Å
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Refine LS restraints |
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