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Open data
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Basic information
Entry | Database: PDB / ID: 7k1c | |||||||||
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Title | TtgR in complex with resveratrol | |||||||||
![]() | HTH-type transcriptional regulator TtgR | |||||||||
![]() | TRANSCRIPTION / TtgR / TetR family / epistasis / resveratrol | |||||||||
Function / homology | ![]() DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bingman, C.A. / Nishikawa, K.K. / Smith, R.W. / Raman, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Epistasis shapes the fitness landscape of an allosteric specificity switch. Authors: Nishikawa, K.K. / Hoppe, N. / Smith, R. / Bingman, C. / Raman, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.4 KB | Display | ![]() |
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PDB format | ![]() | 213.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 793 KB | Display | ![]() |
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Full document | ![]() | 794.2 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k1aC ![]() 7kd8C ![]() 2xdnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 23890.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 nL of protein at 9.8 mg/mL (0.41 millimolar) in 5mM HEPES pH 7.5, 50 mM NaCl, 0.3 mM TCEP and 0.5 millimolar resveratrol was equilibrated against 250 nL 18% PEG4000, 0.2M MgCl2, 0.1M ...Details: 200 nL of protein at 9.8 mg/mL (0.41 millimolar) in 5mM HEPES pH 7.5, 50 mM NaCl, 0.3 mM TCEP and 0.5 millimolar resveratrol was equilibrated against 250 nL 18% PEG4000, 0.2M MgCl2, 0.1M bistris HCl pH 6.5 in a SD2 plate using a Mosquito crystallization robot. Samples were cryoprotected with reservoir solution supplemented with 35% PEG4000. Samples looped in Mitegen micro mounts were flash cooled by immersion in liquid nitrogen. Crystals were grown at 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2018 / Details: 3.0 Undulator C(111) monochromator |
Radiation | Monochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→28.63 Å / Num. obs: 33367 / % possible obs: 99.88 % / Redundancy: 14.4 % / Biso Wilson estimate: 36.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07704 / Rpim(I) all: 0.02123 / Rrim(I) all: 0.07997 / Net I/σ(I): 22.92 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.294 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 3316 / CC1/2: 0.739 / CC star: 0.922 / Rpim(I) all: 0.3446 / Rrim(I) all: 1.339 / % possible all: 99.97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XDN Resolution: 1.9→28.63 Å / SU ML: 0.2689 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3456 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: 42.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.63 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.23568965908 Å / Origin y: -1.72437874147 Å / Origin z: -27.5488402525 Å
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Refinement TLS group | Selection details: all |