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Open data
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Basic information
| Entry | Database: PDB / ID: 5ugt | ||||||
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| Title | Crystal structure of M. tuberculosis InhA inhibited by PT504 | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / bacterial enoyl-ACP reductase / diphenylether / residence time | ||||||
| Function / homology | Function and homology informationtrans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Eltschkner, S. / Pschibul, A. / Spagnuolo, L.A. / Yu, W. / Tonge, P.J. / Kisker, C. | ||||||
| Funding support | Germany, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017Title: Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors. Authors: Spagnuolo, L.A. / Eltschkner, S. / Yu, W. / Daryaee, F. / Davoodi, S. / Knudson, S.E. / Allen, E.K. / Merino, J. / Pschibul, A. / Moree, B. / Thivalapill, N. / Truglio, J.J. / Salafsky, J. / ...Authors: Spagnuolo, L.A. / Eltschkner, S. / Yu, W. / Daryaee, F. / Davoodi, S. / Knudson, S.E. / Allen, E.K. / Merino, J. / Pschibul, A. / Moree, B. / Thivalapill, N. / Truglio, J.J. / Salafsky, J. / Slayden, R.A. / Kisker, C. / Tonge, P.J. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5ugt.cif.gz | 422.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5ugt.ent.gz | 352.5 KB | Display | PDB format |
| PDBx/mmJSON format | 5ugt.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5ugt_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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| Full document | 5ugt_full_validation.pdf.gz | 2.7 MB | Display | |
| Data in XML | 5ugt_validation.xml.gz | 49.4 KB | Display | |
| Data in CIF | 5ugt_validation.cif.gz | 62.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/5ugt ftp://data.pdbj.org/pub/pdb/validation_reports/ug/5ugt | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5mtpC ![]() 5mtqC ![]() 5mtrC ![]() 5ugsC ![]() 5uguC ![]() 2x23S 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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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 269 / Label seq-ID: 22 - 289
NCS ensembles :
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Components
| #1: Protein | Mass: 30726.131 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-XTW / #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: 3.1 Å3/Da / Density % sol: 58.59 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2 M sodium acetate, pH 7.0 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
| Reflection | Resolution: 2.6→46.58 Å / Num. obs: 43766 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.089 / Net I/σ(I): 7.9 |
| Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3.6 % / Num. unique obs: 4566 / CC1/2: 0.299 / % possible all: 98.5 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 2x23 Resolution: 2.6→46.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 35.777 / SU ML: 0.339 / Cross valid method: FREE R-VALUE / ESU R: 0.562 / ESU R Free: 0.285 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 74.339 Å2
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| Refinement step | Cycle: 1 / Resolution: 2.6→46.58 Å
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| Refine LS restraints |
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X-RAY DIFFRACTION
Germany, 1items
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