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Yorodumi- PDB-2b37: Crystal structure of Mycobacterium tuberculosis enoyl reductase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b37 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis enoyl reductase (InhA) inhibited by 5-octyl-2-phenoxyphenol | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / ENOYL REDUCTASE | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Sullivan, T.J. / Truglio, J.J. / Novichenok, P. / Stratton, C. / Zhang, X. / Kaur, T. / Johnson, F. / Boyne, M.S. / Amin, A. | ||||||
Citation | Journal: ACS Chem.Biol. / Year: 2006 Title: High Affinity InhA Inhibitors with Activity against Drug-Resistant Strains of Mycobacterium tuberculosis Authors: Sullivan, T.J. / Truglio, J.J. / Boyne, M.E. / Novichenok, P. / Zhang, X. / Stratton, C. / Li, H.J. / Kaur, T. / Amin, A. / Johnson, F. / Slayden, R.A. / Kisker, C. / Tonge, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b37.cif.gz | 290.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b37.ent.gz | 240.4 KB | Display | PDB format |
PDBx/mmJSON format | 2b37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/2b37 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/2b37 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a tetramer. |
-Components
#1: Protein | Mass: 28554.781 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA / Production host: Escherichia coli (E. coli) References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | #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: 2.3 Å3/Da / Density % sol: 45.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 4000, DMSO, ammonium acetate, NAD+, ADA , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2005 |
Radiation | Monochromator: Pt-coated toroidal Si mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→15 Å / Num. all: 46065 / Num. obs: 44393 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.6→2.666 Å / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.866 / SU B: 14.115 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.532 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
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