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Yorodumi- PDB-5li7: Crystal structure of Mycobacterium tuberculosis CYP126A1 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5li7 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis CYP126A1 in complex with 1-(3-(1H-imidazol-1-yl)propyl)-3-((3s,5s,7s)-adamantan-1-yl)urea | ||||||
Components | Putative cytochrome P450 126 | ||||||
Keywords | OXIDOREDUCTASE / monoxygenase / cytochrome P450 | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Levy, C. / Munro, A.W. / Leys, D. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural Characterization and Ligand/Inhibitor Identification Provide Functional Insights into the Mycobacterium tuberculosis Cytochrome P450 CYP126A1. Authors: Chenge, J.T. / Duyet, L.V. / Swami, S. / McLean, K.J. / Kavanagh, M.E. / Coyne, A.G. / Rigby, S.E. / Cheesman, M.R. / Girvan, H.M. / Levy, C.W. / Rupp, B. / von Kries, J.P. / Abell, C. / Leys, D. / Munro, A.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5li7.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5li7.ent.gz | 148.2 KB | Display | PDB format |
PDBx/mmJSON format | 5li7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/5li7 ftp://data.pdbj.org/pub/pdb/validation_reports/li/5li7 | HTTPS FTP |
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-Related structure data
Related structure data | 5li6C 5li8C 5lieC 1oxaS 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: 46010.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria) Gene: cyp126, MT0802 / Production host: Escherichia coli (E. coli) References: UniProt: P9WPN8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M sodium sulphate, 0.1 M Hepes pH 7.5 and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→57.31 Å / Num. obs: 122489 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.58→1.62 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OXA Resolution: 1.58→57.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.425 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.079 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.426 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→57.31 Å
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Refine LS restraints |
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