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- PDB-5fkn: TetR(D) T103A mutant in complex with anhydrotetracycline and magn... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fkn | ||||||
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Title | TetR(D) T103A mutant in complex with anhydrotetracycline and magnesium, P4(3)2(1)2 | ||||||
![]() | TETRACYCLINE REPRESSOR, CLASS D, T103A MUTANT | ||||||
![]() | 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 | ![]() | 181.7 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fkkC ![]() 5fklC ![]() 5fkmC ![]() 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
#1: Protein | Mass: 23258.307 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.76 % / Description: NONE |
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Crystal grow | Temperature: 295 K / pH: 6.5 Details: 1.4 M (NH4)2SO4, 0.1 M MES PH 6.5, 110 MM 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: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→63.6 Å / Num. obs: 39516 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.6 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4D7M Resolution: 1.8→63.55 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.838 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.143 / 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: 29.745 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→63.55 Å
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Refine LS restraints |
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