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- PDB-5fkk: TetR(D) N82A mutant in complex with anhydrotetracycline and magnesium -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fkk | ||||||
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Title | TetR(D) N82A 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 | ![]() | 182.5 KB | Display | ![]() |
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PDB format | ![]() | 147.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 908.2 KB | Display | ![]() |
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Full document | ![]() | 913 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fklC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23245.309 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 250 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TDC.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TDC.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PG4 / | ||||||||
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#3: Chemical | ChemComp-SO4 / | ||||||||
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-TDC / | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-PGE / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.18 % / Description: NONE |
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Crystal grow | Temperature: 295 K / pH: 7.5 Details: 1.5 M (NH4)2SO4, 0.1 M HEPES PH 7.5, 5% PEG 400, 0.2 M NACL, 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: 1.75→63.3 Å / Num. obs: 43782 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 1.75→1.77 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4D7M Resolution: 1.75→63.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.179 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.132 / 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: 36.433 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→63.25 Å
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Refine LS restraints |
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