+Open data
-Basic information
Entry | Database: PDB / ID: 2xrl | ||||||
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Title | Tet-repressor class D T103A with doxycycline | ||||||
Components | TETRACYCLINE REPRESSOR PROTEIN CLASS D | ||||||
Keywords | TRANSCRIPTION / ANTIBIOTIC RESISTANCE / DNA-BINDING / HELIX-TURN-HELIX | ||||||
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: 1.85 Å | ||||||
Authors | Palm, G.J. / Waack, P. / Hinrichs, W. | ||||||
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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xrl.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xrl.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/2xrl ftp://data.pdbj.org/pub/pdb/validation_reports/xr/2xrl | HTTPS FTP |
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-Related structure data
Related structure data | 4b3aC 6fplC 6fpmC 6ftsC 6qjwC 6qjxC 6rblC 6rbmC 6rcrC 6rgxC 2o7oS 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 / Fragment: RESIDUES 2-208 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH610 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): RB791 / References: UniProt: P0ACT4 | ||||||||||||
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#2: Chemical | #3: Chemical | ChemComp-DXT / ( | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12, 12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO- ...(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAM | Sequence details | C-TERMINAL 10 RESIDUES WERE REMOVED FOR IMPROVED CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.3 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: HANGING DROP VAPOR DIFFUSION WITH 2 UL (14 MG/ML PROTEIN) AND 2 UL (0.6 M NACL, 15 % PEG 4000, 0.1 M MES PH 6.5). CRYSTAL WAS CRYOCOOLED WITH PARAFFIN OIL AS CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC / Detector: CCD / Date: Mar 29, 2007 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / 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→33 Å / Num. obs: 19733 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 9.17 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O7O Resolution: 1.85→32.87 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.238 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.851 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→32.87 Å
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Refine LS restraints |
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