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Yorodumi- PDB-5j3l: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j3l | ||||||||||||
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Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with 1-((2-cyclopentylethyl)sulfonyl)pyrrolidine at 1.66A resolution | ||||||||||||
Components | HTH-type transcriptional regulator EthR | ||||||||||||
Keywords | TRANSCRIPTION / EthR / represor / boosting effect | ||||||||||||
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 / DNA binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å | ||||||||||||
Authors | Blaszczyk, M. / Surade, S. / Nikiforov, P.O. / Abell, C. / Blundell, T.L. | ||||||||||||
Funding support | United Kingdom, United States, 3items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Fragment-Sized EthR Inhibitors Exhibit Exceptionally Strong Ethionamide Boosting Effect in Whole-Cell Mycobacterium tuberculosis Assays. Authors: Nikiforov, P.O. / Blaszczyk, M. / Surade, S. / Boshoff, H.I. / Sajid, A. / Delorme, V. / Deboosere, N. / Brodin, P. / Baulard, A.R. / Barry, C.E. / Blundell, T.L. / Abell, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j3l.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j3l.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 5j3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/5j3l ftp://data.pdbj.org/pub/pdb/validation_reports/j3/5j3l | HTTPS FTP |
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-Related structure data
Related structure data | 5ioyC 5iozC 5ip6C 5ipaC 5j1rC 5j1uC 5j1yC 1t56S S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23781.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ethR, etaR, MT3970 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMC0, UniProt: P9WMC1*PLUS |
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#2: Chemical | ChemComp-6FR / |
#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: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium sulphate, Glycerol, MES / PH range: 6.3 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 5, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.66→60.56 Å / Num. obs: 30632 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Rrim(I) all: 0.053 / Net I/σ(I): 29.7 / Num. measured all: 396935 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T56 Resolution: 1.66→54.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.59 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.087 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 93.41 Å2 / Biso mean: 26.488 Å2 / Biso min: 10.18 Å2
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Refinement step | Cycle: final / Resolution: 1.66→54.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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