+Open data
-Basic information
Entry | Database: PDB / ID: 2ntj | ||||||
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Title | Mycobacterium tuberculosis InhA bound with PTH-NAD adduct | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH | ||||||
Keywords | OXIDOREDUCTASE / InhA / prothionamide / tuberculosis | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wang, F. / Sacchettini, J.C. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2007 Title: Mechanism of thioamide drug action against tuberculosis and leprosy. Authors: Wang, F. / Langley, R. / Gulten, G. / Dover, L.G. / Besra, G.S. / Jacobs, W.R. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ntj.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ntj.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ntj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/2ntj ftp://data.pdbj.org/pub/pdb/validation_reports/nt/2ntj | HTTPS FTP |
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-Related structure data
Related structure data | 2h9iC 2ntvC 1enyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer generated from the dimer in the asymmetric unit |
-Components
#1: Protein | Mass: 28393.562 Da / Num. of mol.: 2 / Mutation: D2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | #3: 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: 3.78 Å3/Da / Density % sol: 67.44 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% MDP, 4% DMSO, 0.1M Hepes, 0.025M Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 121 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 30156 / Num. obs: 30035 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.154 / Rsym value: 0.101 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.45 / Num. unique all: 2980 / Rsym value: 0.145 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ENY Resolution: 2.5→19.99 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.051 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.262 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.562 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.501→2.565 Å / Total num. of bins used: 20
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