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Yorodumi- PDB-5oep: Mycobacterium tuberculosis DprE1 in complex with inhibitor TCA481 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oep | ||||||
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Title | Mycobacterium tuberculosis DprE1 in complex with inhibitor TCA481 | ||||||
Components | Decaprenylphosphoryl-beta-D-ribose oxidase | ||||||
Keywords | OXIDOREDUCTASE / FAD-containing oxidoreductase Decaprenylphosphoarabinose synthesis | ||||||
Function / homology | Function and homology information arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Futterer, K. / Batt, S.M. / Besra, G.S. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oep.cif.gz | 344.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oep.ent.gz | 278.9 KB | Display | PDB format |
PDBx/mmJSON format | 5oep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oep_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5oep_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5oep_validation.xml.gz | 32 KB | Display | |
Data in CIF | 5oep_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/5oep ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oep | HTTPS FTP |
-Related structure data
Related structure data | 5oelC 5oeqC 5w0cC 4kw5S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 52039.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: dprE1, Rv3790 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WJF1, decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IMD / | #5: 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: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M imidazole, 30 - 35% (v/v) polypropyleneglycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→57.6 Å / Num. obs: 42105 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.814 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KW5 Resolution: 2.35→57.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 18.099 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.227 / 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: 63.046 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→57.6 Å
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Refine LS restraints |
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