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Yorodumi- PDB-4trm: Structure of the apo form of InhA from Mycobacterium tuberculosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4trm | ||||||
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Title | Structure of the apo form of InhA from Mycobacterium tuberculosis | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / ENOYL REDUCTASE | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.8 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 | 4trm.cif.gz | 585.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4trm.ent.gz | 485.5 KB | Display | PDB format |
PDBx/mmJSON format | 4trm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4trm_validation.pdf.gz | 489.4 KB | Display | wwPDB validaton report |
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Full document | 4trm_full_validation.pdf.gz | 506.6 KB | Display | |
Data in XML | 4trm_validation.xml.gz | 62.3 KB | Display | |
Data in CIF | 4trm_validation.cif.gz | 89.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/4trm ftp://data.pdbj.org/pub/pdb/validation_reports/tr/4trm | HTTPS FTP |
-Related structure data
Related structure data | 4trnC 4troC 2b35S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 269 / Label seq-ID: 3 - 269
NCS ensembles :
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-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 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P9WGR0, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-MES / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30 % (W/V) PEG 400 0.1 M sodium acetate 0.1 M Na-MES |
-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: Apr 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: 1.8→46.98 Å / Num. all: 136543 / Num. obs: 136543 / % possible obs: 98 % / Redundancy: 3.5 % / Rsym value: 0.058 / Net I/σ(I): 12.55 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.49 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2B35 Resolution: 1.8→35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.519 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.123 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.636 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→35 Å
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Refine LS restraints |
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