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Yorodumi- PDB-4b3a: Tetracycline repressor class D mutant H100A in complex with tetra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b3a | ||||||
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Title | Tetracycline repressor class D mutant H100A in complex with tetracycline | ||||||
Components | TETRACYCLINE REPRESSOR PROTEIN CLASS D | ||||||
Keywords | TRANSCRIPTION / TET-REPRESSOR | ||||||
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: 1.7 Å | ||||||
Authors | Eltschkner, S. / Schindler, S. / Palm, G.J. / Schneider, J. / 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 | 4b3a.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b3a.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 4b3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b3a_validation.pdf.gz | 837.7 KB | Display | wwPDB validaton report |
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Full document | 4b3a_full_validation.pdf.gz | 837.9 KB | Display | |
Data in XML | 4b3a_validation.xml.gz | 11 KB | Display | |
Data in CIF | 4b3a_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/4b3a ftp://data.pdbj.org/pub/pdb/validation_reports/b3/4b3a | HTTPS FTP |
-Related structure data
Related structure data | 2xrlC 6fplC 6fpmC 6ftsC 6qjwC 6qjxC 6rblC 6rbmC 6rcrC 6rgxC 2vkeS 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: 23221.264 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: PWH1590 H100A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791 / References: UniProt: P0ACT4 | ||||||
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#2: Chemical | ChemComp-TAC / | ||||||
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Sequence details | N-TERMINAL MET REMOVED. RESIDUES 209 - 218 REMOVED BY CLONING. | |
-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 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.5 M AMMONIUM SULPHATE, 1 M LITHIUM SULPHATE, 0.1 M MES PH 6.5 |
-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 CCD / Detector: CCD / Date: Apr 17, 2007 / Details: OSMIC MULTILAYER |
Radiation | Monochromator: OSMIC MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.79 Å / Num. obs: 19362 / % possible obs: 82.6 % / Observed criterion σ(I): -3 / Redundancy: 5.86 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.15 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 0.9 / % possible all: 17.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VKE Resolution: 1.7→29.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.479 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.148 / 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: 42.319 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.8 Å
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Refine LS restraints |
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