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Open data
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Basic information
Entry | Database: PDB / ID: 6fpm | ||||||
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Title | TetR(D) T103A mutant in complex with tetracycline 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 | ![]() | 102.5 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xrlC ![]() 4b3aC ![]() 6fplSC ![]() 6ftsC ![]() 6qjwC ![]() 6qjxC ![]() 6rblC ![]() 6rbmC ![]() 6rcrC ![]() 6rgxC 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-TAC / | ||
#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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH 6.5, 24% PEG 400, 70mM MgCl2. 2mM TC, 14.55mg/ml protein |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→64.22 Å / Num. obs: 19026 / % possible obs: 99.6 % / Redundancy: 14.1 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.059 / Net I/σ(I): 24.89 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 13.44 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1353 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FPL Resolution: 1.85→64.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.901 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / 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: 45.825 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→64.21 Å
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Refine LS restraints |
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