+Open data
-Basic information
Entry | Database: PDB / ID: 6rbm | ||||||
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Title | TETR(D) E147A MUTANT IN COMPLEX WITH MINOCYCLINE 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 6rbm.cif.gz | 99.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rbm.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 6rbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/6rbm ftp://data.pdbj.org/pub/pdb/validation_reports/rb/6rbm | HTTPS FTP |
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-Related structure data
Related structure data | 2xrlC 4b3aC 6fplSC 6fpmC 6ftsC 6qjwC 6qjxC 6rblC 6rcrC 6rgxC 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
#1: Protein | Mass: 23230.299 Da / Num. of mol.: 1 / Mutation: A2S, E147A 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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#2: Chemical | ChemComp-MIY / ( | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: precipitant: 0.5M (NH4)2SO4, 0.68M Li2SO4, 0.1M Na-citrate, protein: 0.1mL protein, 0.1mL 2mM minoTc, 0.0005mL 3M MgCl2, 100 mM NaCl, 50 mM Tris pH 8.0, ratio 2/2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→63.3 Å / Num. obs: 13397 / % possible obs: 99.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 43.5 Å2 / Rrim(I) all: 0.053 / Net I/σ(I): 22.74 |
Reflection shell | Resolution: 2.05→2.17 Å / Redundancy: 7.15 % / Mean I/σ(I) obs: 2.46 / Num. unique obs: 2117 / Rrim(I) all: 1.09 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FPL Resolution: 2.05→47.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 17.082 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.208 / 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: 53.247 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→47.9 Å
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Refine LS restraints |
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