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Yorodumi- PDB-6qjw: TetR(D) T103A mutant in complex with 7-chlortetracycline and magnesium -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qjw | ||||||
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Title | TetR(D) T103A mutant in complex with 7-chlortetracycline and magnesium | ||||||
Components | Tetracycline repressor protein class D | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 6qjw.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qjw.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qjw_validation.pdf.gz | 851.8 KB | Display | wwPDB validaton report |
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Full document | 6qjw_full_validation.pdf.gz | 854 KB | Display | |
Data in XML | 6qjw_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 6qjw_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/6qjw ftp://data.pdbj.org/pub/pdb/validation_reports/qj/6qjw | HTTPS FTP |
-Related structure data
Related structure data | 2xrlC 4b3aC 6fplC 6fpmC 6ftsC 6qjxC 6rblC 6rbmC 6rcrC 6rgxC 2tctS 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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-Components
#1: Protein | Mass: 23258.307 Da / Num. of mol.: 1 / Mutation: A2S, T103A 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-CTC / | ||
#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: 2.26 Å3/Da / Density % sol: 45.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Precipitant: 30%PEG 400, 0.1M MES pH 6.5, 60 mM MgCl2. Protein: 12.15 mg/mL protein in 100mM NaCl, 50 mM Tris buffer, pH 8.0, 4mM 7ClTc, 3M MgCl2. Protein/precipitant 1/1 |
-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: Oct 17, 2014 / Details: mirror |
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: 2.1→34.09 Å / Num. obs: 12896 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.85 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.13 / Χ2: 0.97 / Net I/σ(I): 6.85 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.82 % / Rmerge(I) obs: 0.487 / Num. unique obs: 1245 / Χ2: 1.23 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2TCT Resolution: 2.1→34.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.474 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.247 / 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: 31.192 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→34.09 Å
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Refine LS restraints |
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