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- PDB-5fkl: TetR(D) H100A mutant in complex with anhydrotetracycline and magnesium -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fkl | ||||||
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Title | TetR(D) H100A mutant in complex with anhydrotetracycline and magnesium | ||||||
![]() | TETRACYCLINE REPRESSOR, CLASS D | ||||||
![]() | TRANSCRIPTION / REPRESSOR / ANTIBIOTIC RESISTANCE / TETR | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Werten, S. / Schneider, J. / Palm, G.J. / Hinrichs, W. | ||||||
![]() | ![]() 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 | ![]() | 98.1 KB | Display | ![]() |
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PDB format | ![]() | 76.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 824 KB | Display | ![]() |
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Full document | ![]() | 824.6 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fkkC ![]() 5fkmC ![]() 5fknC ![]() 5fkoC ![]() 4d7mS C: citing same article ( 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23221.264 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 70 molecules ![](data/chem/img/TDC.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-TDC / | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-SO4 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.59 % / Description: NONE |
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Crystal grow | Temperature: 295 K Details: 0.4 M (NH4)2SO4, 0.7 M LI2SO4, 0.1 M SODIUM CITRATE, 1 MM 5A,6-ANHYDROTETRACYCLINE, 7.5 MM MGCL2 AT 295 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX SX-165mm / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8031 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→62 Å / Num. obs: 15800 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.5 / % possible all: 99.2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4D7M Resolution: 1.9→62.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.051 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.078 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→62.02 Å
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Refine LS restraints |
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