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- PDB-6qjw: TetR(D) T103A mutant in complex with 7-chlortetracycline and magnesium -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qjw | ||||||
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Title | TetR(D) T103A mutant in complex with 7-chlortetracycline 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 |
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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 | ![]() | 77.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 851.8 KB | Display | ![]() |
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Full document | ![]() | 854 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xrlC ![]() 4b3aC ![]() 6fplC ![]() 6fpmC ![]() 6ftsC ![]() 6qjxC ![]() 6rblC ![]() 6rbmC ![]() 6rcrC ![]() 6rgxC ![]() 2tctS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 23258.307 Da / Num. of mol.: 1 / Mutation: A2S, T103A Source method: isolated from a genetically manipulated source Details: RA1 plasmid / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-CTC / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Precipitant: 30%PEG 400, 0.1M MES pH 6.5, 60 mM MgCl2. Protein: 12.15 mg/mL protein in 100mM NaCl, 50 mM Tris buffer, pH 8.0, 4mM 7ClTc, 3M MgCl2. Protein/precipitant 1/1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 70 / Detector: CCD / Date: Oct 17, 2014 / Details: mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34.09 Å / Num. obs: 12896 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.85 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.13 / Χ2: 0.97 / Net I/σ(I): 6.85 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.82 % / Rmerge(I) obs: 0.487 / Num. unique obs: 1245 / Χ2: 1.23 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2TCT Resolution: 2.1→34.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.474 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.247 / 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: 31.192 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→34.09 Å
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Refine LS restraints |
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