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- PDB-6geo: Crystal structure of Mycobacterium tuberculosis cytochrome P450 C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6geo | |||||||||||||||||||||
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Title | Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP121A1 in complex with Triazole Pyrazole inhibitor 10j | |||||||||||||||||||||
![]() | Mycocyclosin synthase | |||||||||||||||||||||
![]() | OXIDOREDUCTASE / Inhibitor complex P450 / ANTIBIOTIC | |||||||||||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Levy, C.W. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Design and Synthesis of Imidazole and Triazole Pyrazoles asMycobacterium TuberculosisCYP121A1 Inhibitors. Authors: Kishk, S.M. / McLean, K.J. / Sood, S. / Smith, D. / Evans, J.W.D. / Helal, M.A. / Gomaa, M.S. / Salama, I. / Mostafa, S.M. / de Carvalho, L.P.S. / Levy, C.W. / Munro, A.W. / Simons, C. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.4 KB | Display | ![]() |
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PDB format | ![]() | 138.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6geqC ![]() 1n4gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() Strain: CDC 1551 / Oshkosh / Gene: cyp121, MT2336 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | ChemComp-EW2 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 800 nL drops with protein to mother liquor at a ratio of 1 to 1, by vapour diffusion in 1.5 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.16 Å / Num. obs: 76715 / % possible obs: 98.59 % / Redundancy: 18 % / Biso Wilson estimate: 12.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0736 / Rpim(I) all: 0.0176 / Rrim(I) all: 0.0757 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5.45 / Num. unique obs: 7491 / CC1/2: 0.972 / Rpim(I) all: 0.088 / % possible all: 99.59 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N4G Resolution: 1.5→47.16 Å / SU ML: 0.1107 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.5246
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→47.16 Å
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Refine LS restraints |
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LS refinement shell |
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