+Open data
-Basic information
Entry | Database: PDB / ID: 3fnf | ||||||
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Title | Crystal structure of InhA bound to triclosan derivative | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / InhA / triclosan / tuberculosis / Antibiotic resistance / Fatty acid biosynthesis / Lipid synthesis / NAD | ||||||
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: 2.3 Å | ||||||
Authors | Wang, F. | ||||||
Citation | Journal: Chemmedchem / Year: 2009 Title: Triclosan Derivatives: Towards Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis. Authors: Freundlich, J.S. / Wang, F. / Vilcheze, C. / Gulten, G. / Langley, R. / Schiehser, G.A. / Jacobus, D.P. / 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 | 3fnf.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fnf.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 3fnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/3fnf ftp://data.pdbj.org/pub/pdb/validation_reports/fn/3fnf | HTTPS FTP |
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-Related structure data
Related structure data | 3fneC 3fngC 3fnhC 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
#1: Protein | Mass: 28554.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MT1531, MTCY277.05 / Production host: Escherichia coli (E. coli) References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-JPM / #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: 2.49 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 20% PEG 3350, 6% DMSO, 0.1M ADA pH 6.8, and 0.08 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 121 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.91 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 48113 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.087 / Rsym value: 0.103 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.3→2.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3799 / Rsym value: 0.883 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ENY Resolution: 2.3→19.85 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.95 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.256 / 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: 40.206 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.297→2.356 Å / Total num. of bins used: 20
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