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Yorodumi- PDB-3g1o: EthR from Mycobacterium tuberculosis in complex with compound BDM14500 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g1o | ||||||
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Title | EthR from Mycobacterium tuberculosis in complex with compound BDM14500 | ||||||
Components | TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR | ||||||
Keywords | TRANSCRIPTION / TerT family / transcriptional repressor / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Willand, N. / Dirie, B. / Carette, X. / Bifani, P. / Singhal, A. / Desroses, M. / Leroux, F. / Willery, E. / Mathys, V. / Deprez-Poulain, R. ...Willand, N. / Dirie, B. / Carette, X. / Bifani, P. / Singhal, A. / Desroses, M. / Leroux, F. / Willery, E. / Mathys, V. / Deprez-Poulain, R. / Delcroix, G. / Frenois, F. / Aumercier, M. / Locht, C. / Villeret, V. / Deprez, B. / Baulard, A.R. | ||||||
Citation | Journal: NAT.MED. (N.Y.) / Year: 2009 Title: Synthetic EthR inhibitors boost antituberculous activity of ethionamide. Authors: Willand, N. / Dirie, B. / Carette, X. / Bifani, P. / Singhal, A. / Desroses, M. / Leroux, F. / Willery, E. / Mathys, V. / Deprez-Poulain, R. / Delcroix, G. / Frenois, F. / Aumercier, M. / ...Authors: Willand, N. / Dirie, B. / Carette, X. / Bifani, P. / Singhal, A. / Desroses, M. / Leroux, F. / Willery, E. / Mathys, V. / Deprez-Poulain, R. / Delcroix, G. / Frenois, F. / Aumercier, M. / Locht, C. / Villeret, V. / Deprez, B. / Baulard, A.R. #1: Journal: Tuberculosis / Year: 2006 Title: Insights into mechanisms of induction and ligands recognition in the transcriptional repressor EthR from Mycobacterium tuberculosis. Authors: Frenois, F. / Baulard, A.R. / Villeret, V. #2: Journal: Mol.Cell / Year: 2004 Title: Structure of EthR in a ligand bound conformation reveals therapeutic perspectives against tuberculosis. Authors: Frenois, F. / Engohang-Ndong, J. / Locht, C. / Baulard, A.R. / Villeret, V. #3: Journal: Mol.Microbiol. / Year: 2004 Title: EthR, a repressor of the TetR/CamR family implicated in ethionamide resistance in mycobacteria, octamerizes cooperatively on its operator. Authors: Engohang-Ndong, J. / Baillat, D. / Aumercier, M. / Bellefontaine, F. / Besra, G.S. / Locht, C. / Baulard, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g1o.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g1o.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 3g1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/3g1o ftp://data.pdbj.org/pub/pdb/validation_reports/g1/3g1o | HTTPS FTP |
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-Related 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: 27979.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ethR, MT3970, Rv3855 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96222, UniProt: P9WMC1*PLUS |
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#2: Chemical | ChemComp-RF1 / |
#3: 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: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.17 M ammonium sulfate, 0.085 M Na-cacodylate (pH 6.5), 15% glycerol, and 25% polyethylene glycol 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.85→19.42 Å / Num. all: 20428 / Num. obs: 20428 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.85→1.898 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→19.42 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 7.637 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.15 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.567 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→19.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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