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Yorodumi- PDB-5ibf: Crystal structure Mycobacterium tuberculosis CYP121 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ibf | ||||||
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Title | Crystal structure Mycobacterium tuberculosis CYP121 in complex with inhibitor fragment 19a | ||||||
Components | Mycocyclosin synthase | ||||||
Keywords | OXIDOREDUCTASE / Mycobacterium tuberculosis / CYP121 / Fragment based inhibitor screening | ||||||
Function / homology | Function and homology information mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Levy, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. Authors: Kavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C.W. / Marino, L.B. / de Carvalho, L.P. / Chan, D.S. / Hudson, S.A. / Surade, S. / Leys, D. / Munro, A.W. / Abell, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ibf.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ibf.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 5ibf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ibf_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5ibf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5ibf_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5ibf_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/5ibf ftp://data.pdbj.org/pub/pdb/validation_reports/ib/5ibf | HTTPS FTP |
-Related structure data
Related structure data | 5edtC 5ibdC 5ibeC 5ibgC 5ibhC 5ibiC 5ibjC 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 (bacteria) / Gene: cyp121, MT2336 / Production host: Escherichia coli (E. coli) References: UniProt: P9WPP6, UniProt: P9WPP7*PLUS, EC: 1.14.21.9 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-HEM / | ||
#4: Chemical | #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: 2.7 Å3/Da / Density % sol: 54.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.5-2.1 M ammonium sulfate and 0.1 M sodium MES or Cacodylate from pH 5.5-6.15 PH range: 5.5 - 6.15 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9174 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.378 Å / Num. obs: 99239 / % possible obs: 99.59 % / Redundancy: 26 % / CC1/2: 1 / Rmerge(I) obs: 0.0869 / Net I/σ(I): 22.01 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INHOUSE Resolution: 1.7→47.378 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→47.378 Å
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Refine LS restraints |
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LS refinement shell |
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