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- PDB-5oel: Mycobacterium tuberculosis DprE1 mutant Y314C in complex with TCA1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oel | ||||||
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Title | Mycobacterium tuberculosis DprE1 mutant Y314C in complex with TCA1 | ||||||
![]() | Decaprenylphosphoryl-beta-D-ribose oxidase | ||||||
![]() | OXIDOREDUCTASE / FAD-containing oxidoreductase Decaprenylphosphoarabinose synthesis | ||||||
Function / homology | ![]() decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Futterer, K. / Batt, S.M. / Besra, G.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Determinants of the Inhibition of DprE1 and CYP2C9 by Antitubercular Thiophenes. Authors: Liu, R. / Lyu, X. / Batt, S.M. / Hsu, M.H. / Harbut, M.B. / Vilcheze, C. / Cheng, B. / Ajayi, K. / Yang, B. / Yang, Y. / Guo, H. / Lin, C. / Gan, F. / Wang, C. / Franzblau, S.G. / Jacobs, W. ...Authors: Liu, R. / Lyu, X. / Batt, S.M. / Hsu, M.H. / Harbut, M.B. / Vilcheze, C. / Cheng, B. / Ajayi, K. / Yang, B. / Yang, Y. / Guo, H. / Lin, C. / Gan, F. / Wang, C. / Franzblau, S.G. / Jacobs, W.R. / Besra, G.S. / Johnson, E.F. / Petrassi, M. / Chatterjee, A.K. / Futterer, K. / Wang, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.8 KB | Display | ![]() |
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PDB format | ![]() | 277 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5oepC ![]() 5oeqC ![]() 5w0cC ![]() 4kw5S 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 51979.812 Da / Num. of mol.: 2 / Mutation: Y314C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CDC 1551 / Oshkosh / Gene: dprE1, MT3898 / Production host: ![]() ![]() References: UniProt: P9WJF0, decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M imidazole pH 7.5, 30 - 35% (vol/vol) polypropyleneglycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→83.7 Å / Num. obs: 50740 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/av σ(I): 13.1 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.811 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KW5 Resolution: 2.2→83.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.506 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.188 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.12 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→83.7 Å
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Refine LS restraints |
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