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Yorodumi- PDB-6ho7: TRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ho7 | ||||||
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Title | TRANSCRIPTIONAL REPRESSOR ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH BDM44814 | ||||||
Components | HTH-type transcriptional regulator EthR | ||||||
Keywords | DNA BINDING PROTEIN / HELIX-TURN-HELIX / TETR-FAMILY / COMPLEX / INHIBITOR / DRUG DESIGN / TUBERCULOSIS / ETHIONAMIDE | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis CDC1551 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Wintjens, R. / Wohlkonig, A. | ||||||
Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2018 Title: A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR. Authors: Tanina, A. / Wohlkonig, A. / Soror, S.H. / Flipo, M. / Villemagne, B. / Prevet, H. / Deprez, B. / Moune, M. / Peree, H. / Meyer, F. / Baulard, A.R. / Willand, N. / Wintjens, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ho7.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ho7.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ho7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ho7_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 6ho7_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 6ho7_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6ho7_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/6ho7 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/6ho7 | HTTPS FTP |
-Related structure data
Related structure data | 6hnxC 6hnzC 6ho0C 6ho1C 6ho2C 6ho3C 6ho4C 6ho5C 6ho6C 6ho8C 6ho9C 6hoaC 6hobC 6hocC 6hodC 6hoeC 6hofC 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: 24927.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria) Gene: ethR, etaR, MT3970 / Variant: CDC 1551 / Oshkosh / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P9WMC0 |
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#2: Chemical | ChemComp-GHQ / ~{ |
#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: 2.38 Å3/Da / Density % sol: 48.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.7 / Details: 1.4-1.6 ammonium sulfate, 15% glycerol, 100 mM MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33.7 Å / Num. obs: 9145 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1280 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Resolution: 2.5→33.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.027 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.252 / 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: 39.707 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→33.55 Å
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Refine LS restraints |
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