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- PDB-5mru: TetR(class A) in complex with 5a,6-anhydrotetracycline and magnesium -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mru | ||||||
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Title | TetR(class A) in complex with 5a,6-anhydrotetracycline and magnesium | ||||||
![]() | Tetracycline Repressor, class A | ||||||
![]() | TRANSCRIPTION / Repressor / Tetracycline / helix-turn-helix | ||||||
Function / homology | ![]() response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hinrichs, W. / Palm, G.J. | ||||||
![]() | ![]() Title: TetR(class A) in complex with 5a,6-anhydrotetracycline and magnesium Authors: Hinrichs, W. / Palm, G.J. #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 | ![]() | 83.1 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808.6 KB | Display | ![]() |
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Full document | ![]() | 811.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vprS S: Starting model for refinement |
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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
#1: Protein | Mass: 23315.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-TDC / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2uL complex [10uL TetR(A) with 39.6 mg/ml TetR(A) + 50uL anTC (2mM in 200mM NaCl) + 0.25uL MgCl2 (3M) + 40uL H2O] + Reservoir 1uL (0.026mM (NH4)H2HPO4) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: May 1, 2008 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.505→54.65 Å / Num. obs: 7877 / % possible obs: 98.2 % / Observed criterion σ(I): -1 / Redundancy: 4.8 % / Biso Wilson estimate: 56.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Net I/σ(I): 12.37 |
Reflection shell | Resolution: 2.505→2.66 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.02 / CC1/2: 0.444 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2vpr Resolution: 2.55→54.65 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 29.357 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.319 / 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: 62.846 Å2
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Refinement step | Cycle: 1 / Resolution: 2.55→54.65 Å
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Refine LS restraints |
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