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Open data
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Basic information
Entry | Database: PDB / ID: 6rgx | ||||||
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Title | TETR(D) N82A MUTANT IN COMPLEX WITH DOXYCYCLINE 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 | ![]() | 184.2 KB | Display | ![]() |
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PDB format | ![]() | 146.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 878 KB | Display | ![]() |
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Full document | ![]() | 884.2 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xrlC ![]() 4b3aC ![]() 6fplC ![]() 6fpmC ![]() 6ftsC ![]() 6qjwC ![]() 6qjxC ![]() 6rblC ![]() 6rbmC ![]() 6rcrC ![]() 5fkkS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 208 / Label seq-ID: 1 - 207
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23245.309 Da / Num. of mol.: 2 / Mutation: A2S, N82A Source method: isolated from a genetically manipulated source Details: RA1 plasmid / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 276 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/DXT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/DXT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-DXT / ( | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: precipitant: 0.1 M HEPES pH 7.5, 1.75M (NH4)2SO4, 5% PEG 400, 0.2M NaCl, protein: 0.1mL protein, 0.3mL 2mM doxyTc, 0.001mL 3M MgCl2, 100mM NaCl, 50mM Tris, pH 8.0, Protein/precipitant 2/2 |
-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: Aug 5, 2011 |
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: 1.8→32.94 Å / Num. obs: 40487 / % possible obs: 99.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.043 / Rrim(I) all: 0.149 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5722 / Rpim(I) all: 0.467 / Rrim(I) all: 1.052 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FKK Resolution: 1.8→31.98 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.527 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.135 / 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: 27.671 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→31.98 Å
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Refine LS restraints |
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