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Open data
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Basic information
Entry | Database: PDB / ID: 2xrl | ||||||
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Title | Tet-repressor class D T103A with doxycycline | ||||||
![]() | TETRACYCLINE REPRESSOR PROTEIN CLASS D | ||||||
![]() | TRANSCRIPTION / ANTIBIOTIC RESISTANCE / DNA-BINDING / HELIX-TURN-HELIX | ||||||
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 | ![]() ![]() | ||||||
![]() | Palm, G.J. / Waack, P. / Hinrichs, W. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.1 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 851.3 KB | Display | ![]() |
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Full document | ![]() | 854.6 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b3aC ![]() 6fplC ![]() 6fpmC ![]() 6ftsC ![]() 6qjwC ![]() 6qjxC ![]() 6rblC ![]() 6rbmC ![]() 6rcrC ![]() 6rgxC ![]() 2o7oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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Components
#1: Protein | Mass: 23258.307 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-208 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||||||
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#2: Chemical | #3: Chemical | ChemComp-DXT / ( | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12, 12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO- ...(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAM | Sequence details | C-TERMINAL 10 RESIDUES WERE REMOVED FOR IMPROVED CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.3 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: HANGING DROP VAPOR DIFFUSION WITH 2 UL (14 MG/ML PROTEIN) AND 2 UL (0.6 M NACL, 15 % PEG 4000, 0.1 M MES PH 6.5). CRYSTAL WAS CRYOCOOLED WITH PARAFFIN OIL AS CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU-MSC / Detector: CCD / Date: Mar 29, 2007 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / 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→33 Å / Num. obs: 19733 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 9.17 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 88.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2O7O Resolution: 1.85→32.87 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.238 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.851 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→32.87 Å
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Refine LS restraints |
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