+
Open data
-
Basic information
Entry | Database: PDB / ID: 6qjx | ||||||
---|---|---|---|---|---|---|---|
Title | TetR(D) T103A mutant in complex with minocycline and magnesium | ||||||
![]() | Tetracycline repressor protein class D | ||||||
![]() | TRANSCRIPTION / TRANSCRIPTION REGULATION | ||||||
Function / homology | ![]() transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hinrichs, W. / Palm, G.J. / Berndt, L. / Girbardt, B. | ||||||
![]() | ![]() Title: Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding. Authors: Palm, G.J. / Buchholz, I. / Werten, S. / Girbardt, B. / Berndt, L. / Delcea, M. / Hinrichs, W. #1: ![]() Title: Modular organisation of inducer recognition and allostery in the tetracycline repressor. Authors: Werten, S. / Schneider, J. / Palm, G.J. / Hinrichs, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2xrlC ![]() 4b3aC ![]() 6fplC ![]() 6fpmC ![]() 6ftsC ![]() 6qjwC ![]() 6rblC ![]() 6rbmC ![]() 6rcrC ![]() 6rgxC ![]() 2tctS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 23258.307 Da / Num. of mol.: 1 / Mutation: A2S, T103A Source method: isolated from a genetically manipulated source Details: RA1-plasmid / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-MIY / ( | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.75 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Precipitant: 0.1 M MES pH 6.5, 24% PEG 400, 70 mM MgCl2. Protein: 14.55 mg/mL protein in 100mM NaCl, 50 mM Tris buffer, pH 8.0, with 2mM MinoTc, 0.38 uL 3M MgCl2. Precipitant/protein 1/4. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 3, 2011 / Details: NULL |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→57 Å / Num. obs: 11944 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.85 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.15 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.54 / Num. unique obs: 1928 / % possible all: 95.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2TCT Resolution: 2.1→42.36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.993 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.701 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→42.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|