+Open data
-Basic information
Entry | Database: PDB / ID: 6rgx | ||||||
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Title | TETR(D) N82A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM | ||||||
Components | Tetracycline repressor protein class D | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION | ||||||
Function / homology | Function and homology information response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hinrichs, W. / Palm, G.J. / Berndt, L. / Girbardt, B. | ||||||
Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2020 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: Journal: FEBS J. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rgx.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rgx.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 6rgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/6rgx ftp://data.pdbj.org/pub/pdb/validation_reports/rg/6rgx | HTTPS FTP |
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-Related structure data
Related structure data | 2xrlC 4b3aC 6fplC 6fpmC 6ftsC 6qjwC 6qjxC 6rblC 6rbmC 6rcrC 5fkkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 2 - 208 / Label seq-ID: 1 - 207
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23245.309 Da / Num. of mol.: 2 / Mutation: A2S, N82A Source method: isolated from a genetically manipulated source Details: RA1 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Plasmid: pWH1950 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ACT4 |
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-Non-polymers , 6 types, 276 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-DXT / ( | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: precipitant: 0.1 M HEPES pH 7.5, 1.75M (NH4)2SO4, 5% PEG 400, 0.2M NaCl, protein: 0.1mL protein, 0.3mL 2mM doxyTc, 0.001mL 3M MgCl2, 100mM NaCl, 50mM Tris, pH 8.0, Protein/precipitant 2/2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 70 / Detector: CCD / Date: Aug 5, 2011 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32.94 Å / Num. obs: 40487 / % possible obs: 99.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.043 / Rrim(I) all: 0.149 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5722 / Rpim(I) all: 0.467 / Rrim(I) all: 1.052 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FKK Resolution: 1.8→31.98 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.527 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.135 / 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: 27.671 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→31.98 Å
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Refine LS restraints |
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