+Open data
-Basic information
Entry | Database: PDB / ID: 5o4k | ||||||
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Title | Crystal structure of P450 CYP121 in complex with compound 6b. | ||||||
Components | Mycocyclosin synthase | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 Redox Inhibitor | ||||||
Function / homology | Function and homology information mycocyclosin synthase / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis CDC1551 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Levy, C.W. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Novel Aryl Substituted Pyrazoles as Small Molecule Inhibitors of Cytochrome P450 CYP121A1: Synthesis and Antimycobacterial Evaluation. Authors: Taban, I.M. / Elshihawy, H.E.A.E. / Torun, B. / Zucchini, B. / Williamson, C.J. / Altuwairigi, D. / Ngu, A.S.T. / McLean, K.J. / Levy, C.W. / Sood, S. / Marino, L.B. / Munro, A.W. / de ...Authors: Taban, I.M. / Elshihawy, H.E.A.E. / Torun, B. / Zucchini, B. / Williamson, C.J. / Altuwairigi, D. / Ngu, A.S.T. / McLean, K.J. / Levy, C.W. / Sood, S. / Marino, L.B. / Munro, A.W. / de Carvalho, L.P.S. / Simons, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o4k.cif.gz | 183 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o4k.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 5o4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o4k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5o4k_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5o4k_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 5o4k_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/5o4k ftp://data.pdbj.org/pub/pdb/validation_reports/o4/5o4k | HTTPS FTP |
-Related structure data
Related structure data | 5o4lC 5op9C 5opaC 1n40S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 43305.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria) Gene: cyp121, MT2336 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP6, EC: 1.14.21.9 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-9KE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.5 to 2.1 M ammonium sulfate and 0.1 M sodium MES or Cacodylate from pH 5.5 to 6.15 PH range: 5.5 - 6.15 / Temp details: Cold room |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→67.23 Å / Num. obs: 76451 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.99 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.026 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.5→1.56 Å / Redundancy: 20 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 3 / Num. unique obs: 7498 / CC1/2: 0.909 / Rpim(I) all: 0.243 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N40 Resolution: 1.5→67.23 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.113 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.999 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→67.23 Å
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Refine LS restraints |
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