+Open data
-Basic information
Entry | Database: PDB / ID: 6yuu | ||||||
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Title | Crystal structure of M. tuberculosis InhA inhibited by SKTS1 | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / bacterial enoyl-ACP reductase / diphenylether / residence time | ||||||
Function / homology | Function and homology information trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / response to antibiotic Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis CDC1551 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Eltschkner, S. / Schiebel, J. / Kehrein, J. / Le, T.A. / Davoodi, S. / Merget, B. / Weinrich, J.D. / Tonge, P.J. / Engels, B. / Sotriffer, C.A. / Kisker, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2021 Title: A Long Residence Time Enoyl-Reductase Inhibitor Explores an Extended Binding Region with Isoenzyme-Dependent Tautomer Adaptation and Differential Substrate-Binding Loop Closure. Authors: Eltschkner, S. / Kehrein, J. / Le, T.A. / Davoodi, S. / Merget, B. / Basak, S. / Weinrich, J.D. / Schiebel, J. / Tonge, P.J. / Engels, B. / Sotriffer, C. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yuu.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yuu.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 6yuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yuu_validation.pdf.gz | 963 KB | Display | wwPDB validaton report |
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Full document | 6yuu_full_validation.pdf.gz | 965.2 KB | Display | |
Data in XML | 6yuu_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6yuu_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yuu ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yuu | HTTPS FTP |
-Related structure data
Related structure data | 6yurC 2x23S 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: 30726.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal His6tag Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria) Gene: inhA, MT1531 / Production host: Escherichia coli (E. coli) References: UniProt: P9WGR0, enoyl-[acyl-carrier-protein] reductase (NADH) |
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-Non-polymers , 5 types, 302 molecules
#2: Chemical | ChemComp-NAD / | ||||
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#3: Chemical | ChemComp-F9T / | ||||
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.96 Å3/Da / Density % sol: 58.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 100 mM Tris, pH 8.4 3 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→47.76 Å / Num. obs: 23730 / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.041 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.01→2.12 Å / Rmerge(I) obs: 1.095 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3383 / Rpim(I) all: 0.254 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2X23 Resolution: 2.01→47.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.414 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.953 Å2
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Refinement step | Cycle: 1 / Resolution: 2.01→47.7 Å
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Refine LS restraints |
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