[English] 日本語
Yorodumi- PDB-5jfo: Structure of the M.tuberculosis enoyl-reductase InhA in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jfo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the M.tuberculosis enoyl-reductase InhA in complex with GSK625 | |||||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / antitubercular / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information trans-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 | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.907 Å | |||||||||
Authors | Gulten, G. / Sacchettini, J.C. | |||||||||
Funding support | United States, Spain, 2items
| |||||||||
Citation | Journal: Ebiomedicine / Year: 2016 Title: Antitubercular drugs for an old target: GSK693 as a promising InhA direct inhibitor. Authors: Martinez-Hoyos, M. / Perez-Herran, E. / Gulten, G. / Encinas, L. / Alvarez-Gomez, D. / Alvarez, E. / Ferrer-Bazaga, S. / Garcia-Perez, A. / Ortega, F. / Angulo-Barturen, I. / Rullas- ...Authors: Martinez-Hoyos, M. / Perez-Herran, E. / Gulten, G. / Encinas, L. / Alvarez-Gomez, D. / Alvarez, E. / Ferrer-Bazaga, S. / Garcia-Perez, A. / Ortega, F. / Angulo-Barturen, I. / Rullas-Trincado, J. / Blanco Ruano, D. / Torres, P. / Castaneda, P. / Huss, S. / Fernandez Menendez, R. / Gonzalez Del Valle, S. / Ballell, L. / Barros, D. / Modha, S. / Dhar, N. / Signorino-Gelo, F. / McKinney, J.D. / Garcia-Bustos, J.F. / Lavandera, J.L. / Sacchettini, J.C. / Jimenez, M.S. / Martin-Casabona, N. / Castro-Pichel, J. / Mendoza-Losana, A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jfo.cif.gz | 215.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jfo.ent.gz | 173.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/5jfo ftp://data.pdbj.org/pub/pdb/validation_reports/jf/5jfo | HTTPS FTP |
---|
-Related structure data
Related structure data | 1enyS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28554.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)3 References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-6KA / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.85 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.1 M Sodium malonate, 0.1 M Hepes pH 7.0, 0.5% (v/v) Jeffamine ED-2001 pH 7.0 |
-Data collection
Diffraction | Mean temperature: 120 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 20, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 39516 / % possible obs: 98 % / Redundancy: 3.9 % / Biso Wilson estimate: 73.53 Å2 / Rmerge(I) obs: 0.101 / Χ2: 1.602 / Net I/av σ(I): 16.254 / Net I/σ(I): 9.8 / Num. measured all: 152228 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ENY Resolution: 2.907→34.686 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.08
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 29.355 Å2 / ksol: 0.297 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.57 Å2 / Biso mean: 73.91 Å2 / Biso min: 33.82 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.907→34.686 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|