+Open data
-Basic information
Entry | Database: PDB / ID: 4qxm | ||||||
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Title | Crystal structure of the InhA:GSK_SB713 complex | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Rossman fold / enoyl-ACP reductase / NADH binding / 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 H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å | ||||||
Authors | Gulten, G. / Sacchettini, J.C. | ||||||
Citation | Journal: Chemmedchem / Year: 2016 Title: N-Benzyl-4-((heteroaryl)methyl)benzamides: A New Class of Direct NADH-Dependent 2-trans Enoyl-Acyl Carrier Protein Reductase (InhA) Inhibitors with Antitubercular Activity. Authors: Guardia, A. / Gulten, G. / Fernandez, R. / Gomez, J. / Wang, F. / Convery, M. / Blanco, D. / Martinez, M. / Perez-Herran, E. / Alonso, M. / Ortega, F. / Rullas, J. / Calvo, D. / Mata, L. / ...Authors: Guardia, A. / Gulten, G. / Fernandez, R. / Gomez, J. / Wang, F. / Convery, M. / Blanco, D. / Martinez, M. / Perez-Herran, E. / Alonso, M. / Ortega, F. / Rullas, J. / Calvo, D. / Mata, L. / Young, R. / Sacchettini, J.C. / Mendoza-Losana, A. / Remuinan, M. / Ballell Pages, L. / Castro-Pichel, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qxm.cif.gz | 404.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qxm.ent.gz | 332.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qxm_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4qxm_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4qxm_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 4qxm_validation.cif.gz | 57.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/4qxm ftp://data.pdbj.org/pub/pdb/validation_reports/qx/4qxm | HTTPS FTP |
-Related structure data
Related structure data | 1enyS 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
#1: Protein | Mass: 28554.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: inhA, MTCY277.05, Rv1484 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WGR1, 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: 2.4 Å3/Da / Density % sol: 48.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1 M N-(2-acetamido)iminodiacetic acid, pH 6.8, 6% v/v DMSO, 16% w/v PEG3350, 0.18 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2007 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.196→77.776 Å / Num. all: 55342 / Num. obs: 48167 / % possible obs: 86.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 32.15 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.196→2.28 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.53 / % possible all: 60.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ENY Resolution: 2.196→45.575 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 26.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.196→45.575 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -17.0224 Å / Origin y: -3.693 Å / Origin z: 15.5926 Å
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Refinement TLS group | Selection details: all |