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- PDB-8b4e: ToxR bacterial transcriptional regulator bound to 25 bp toxT prom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b4e | |||||||||||||||
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Title | ToxR bacterial transcriptional regulator bound to 25 bp toxT promoter DNA | |||||||||||||||
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![]() | DNA BINDING PROTEIN / bacterial transcription / activation complex | |||||||||||||||
Function / homology | ![]() phosphorelay response regulator activity / regulation of DNA-templated transcription / DNA binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Canals, A. / Pieretti, S. / Muriel, M. / El Yaman, N. / Fabrega-Ferrer, M. / Perez-Luque, R. / Krukonis, E.S. / Coll, M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites. Authors: Canals, A. / Pieretti, S. / Muriel-Masanes, M. / El Yaman, N. / Plecha, S.C. / Thomson, J.J. / Fabrega-Ferrer, M. / Perez-Luque, R. / Krukonis, E.S. / Coll, M. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102 KB | Display | ![]() |
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PDB format | ![]() | 61.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.6 KB | Display | ![]() |
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Full document | ![]() | 453.4 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b4bC ![]() 8b4cC ![]() 8b4dC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12703.462 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 7634.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: DNA chain | | Mass: 7716.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 4000, 0.3 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→81.18 Å / Num. obs: 9545 / % possible obs: 99.17 % / Redundancy: 4 % / Biso Wilson estimate: 116.07 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.02 |
Reflection shell | Resolution: 3.25→3.36 Å / Rmerge(I) obs: 0.533 / Num. unique obs: 889 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB in deposition Resolution: 3.25→81.18 Å / SU ML: 0.5785 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.8886 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.73 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→81.18 Å
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Refine LS restraints |
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LS refinement shell |
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