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Yorodumi- PDB-5oil: InhA (T2A mutant) complexed with 1-cyclohexyl-3-(pyridin-3-ylmeth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oil | ||||||
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Title | InhA (T2A mutant) complexed with 1-cyclohexyl-3-(pyridin-3-ylmethyl)urea | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / Inhibitor / complex / fragment based drug discovery / tuberculosis | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.76 Å | ||||||
Authors | Convery, M.A. | ||||||
Citation | Journal: ChemMedChem / Year: 2018 Title: Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA. Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / ...Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / Green, S.R. / Huggett, M. / Barros, D. / Wyatt, P.G. / Ray, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oil.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oil.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 5oil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oil_validation.pdf.gz | 749.3 KB | Display | wwPDB validaton report |
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Full document | 5oil_full_validation.pdf.gz | 750.5 KB | Display | |
Data in XML | 5oil_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5oil_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/5oil ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oil | HTTPS FTP |
-Related structure data
Related structure data | 5oicC 5oifC 5oimC 5oinC 5oioC 5oipC 5oiqC 5oirC 5oisC 5oitC C: citing same article (ref.) |
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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: 28524.754 Da / Num. of mol.: 1 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli) References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-9VW / |
#4: Chemical | ChemComp-ETX / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 35-42% Ethoxyethanol and 0.1M Mes pH 6.5-6.8. 5% glycerol used as cryoprotectant. Crystals were soaked to obtain ligand complex. PH range: 6.5-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→46.77 Å / Num. obs: 10717 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 51.38 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.251 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.76→2.95 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1885 / CC1/2: 0.818 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 2.76→46.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.893 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.514 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 4.839 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.293
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Displacement parameters | Biso mean: 30.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.76→46.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 45.2767 Å / Origin y: 47.8707 Å / Origin z: -88.2972 Å
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Refinement TLS group | Selection details: { A|* } |