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- PDB-5li8: Crystal structure of Mycobacterium tuberculosis CYP126A1 in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5li8 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis CYP126A1 in complex with ketoconazole | ||||||
![]() | Putative cytochrome P450 126 | ||||||
![]() | OXIDOREDUCTASE / monoxygenase / cytochrome P450 | ||||||
Function / homology | ![]() Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Levy, C. / Munro, A.W. / Leys, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.1 KB | Display | ![]() |
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PDB format | ![]() | 79.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5li6C ![]() 5li7C ![]() 5lieC ![]() 1oxaS 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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Unit cell |
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Components
#1: Protein | Mass: 46010.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cyp126, MT0802 / Production host: ![]() ![]() References: UniProt: P9WPN8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-KKK / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2 M sodium sulphate, 0.1 M Tris, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→43.86 Å / Num. obs: 37754 / % possible obs: 92.47 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.83→1.88 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.2 / % possible all: 59.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OXA Resolution: 1.83→43.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.335 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.113 / 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: 13.966 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→43.86 Å
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Refine LS restraints |
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