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Yorodumi- PDB-4tro: Structure of the enoyl-ACP reductase of Mycobacterium tuberculosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tro | ||||||
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Title | Structure of the enoyl-ACP reductase of Mycobacterium tuberculosis InhA, inhibited with the active metabolite of isoniazid | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / isoniazid | ||||||
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 / 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: 1.4 Å | ||||||
Authors | Chollet, A. / Julien, S. / Mourey, L. / Maveyraud, L. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Crystal structure of the enoyl-ACP reductase of Mycobacterium tuberculosis (InhA) in the apo-form and in complex with the active metabolite of isoniazid pre-formed by a biomimetic approach. Authors: Chollet, A. / Mourey, L. / Lherbet, C. / Delbot, A. / Julien, S. / Baltas, M. / Bernadou, J. / Pratviel, G. / Maveyraud, L. / Bernardes-Genisson, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tro.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tro.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 4tro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/4tro ftp://data.pdbj.org/pub/pdb/validation_reports/tr/4tro | HTTPS FTP |
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-Related structure data
Related structure data | 4trmC 4trnC 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28554.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: M9TGV3, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) |
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-Non-polymers , 6 types, 276 molecules
#2: Chemical | ChemComp-NAD / | ||||||
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#3: Chemical | ChemComp-ZID / | ||||||
#4: Chemical | #5: Chemical | ChemComp-DMS / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 8-10 % (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium citrate, 0.1 M Na HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.72 Å / Num. obs: 77041 / % possible obs: 99.6 % / Redundancy: 10.7 % / Rsym value: 0.055 / Net I/σ(I): 21.11 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 0.716 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1eny Resolution: 1.4→40 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.568 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / 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: 31.764 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→40 Å
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Refine LS restraints |
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