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Yorodumi- PDB-2xc3: X-ray structure of Mycobacterium tuberculosis cyp125 bound to the... -
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-Basic information
Entry | Database: PDB / ID: 2xc3 | ||||||
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Title | X-ray structure of Mycobacterium tuberculosis cyp125 bound to the reverse type I inhibitor | ||||||
Components | PUTATIVE CYTOCHROME P450 125 | ||||||
Keywords | OXIDOREDUCTASE / METAL-BINDING | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / biological process involved in interaction with host / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ouellet, H. / Kells, P.M. / Ortiz de Montellano, P.R. / Podust, L.M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Reverse Type I Inhibitor of Mycobacteriumtuberculosis Cyp125A1. Authors: Ouellet, H. / Kells, P.M. / Ortiz de Montellano, P.R. / 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 | 2xc3.cif.gz | 206.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xc3.ent.gz | 162.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xc3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2xc3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2xc3_validation.xml.gz | 24 KB | Display | |
Data in CIF | 2xc3_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xc3 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xc3 | HTTPS FTP |
-Related structure data
Related structure data | 2x5lSC 2xn8C 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
#1: Protein | Mass: 47593.508 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-433 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCWORI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): HMS174 References: UniProt: P63709, UniProt: P9WPP1*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-RT8 / | ||||
#4: Water | ChemComp-HOH / | ||||
Compound details | ENGINEEREDNonpolymer details | A-[(4-METHYLCYCLOHEXYL)CARBONYL AMINO]-N-4-PYRIDINYL-1H-INDOLE-3-PROPANAMIDE (RT8): REVERSE TYPE I ...A-[(4-METHYLCYCL | Sequence details | FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. MUTATIONS V17M AND C429L ARE ENGINEERED. 6XHIS TAG ...FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. MUTATIONS V17M AND C429L ARE ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 5.5 Details: 2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS, PH 5.5, 0.5 M NACL, 4 DEG. CELSIUS |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 4, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11588 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 56093 / % possible obs: 91.9 % / Observed criterion σ(I): 1.5 / Redundancy: 7.1 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 7.5 / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X5L Resolution: 1.5→46.58 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.113 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 233-237 ARE DISORDERED.
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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: 16.009 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→46.58 Å
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Refine LS restraints |
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