+Open data
-Basic information
Entry | Database: PDB / ID: 4v2f | |||||||||
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Title | Tetracycline repressor TetR(D), unliganded | |||||||||
Components | TETRACYCLINE REPRESSOR PROTEIN CLASS D | |||||||||
Keywords | TRANSCRIPTION / REPRESSOR / ANTIBIOTIC RESISTANCE / TETR | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Werten, S. / Orth, P. / Saenger, W. / Hinrichs, W. | |||||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Tetracycline Repressor Allostery Does not Depend on Divalent Metal Recognition. Authors: Werten, S. / Dalm, D. / Palm, G.J. / Grimm, C.C. / Hinrichs, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v2f.cif.gz | 48.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v2f.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 4v2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v2f_validation.pdf.gz | 424.6 KB | Display | wwPDB validaton report |
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Full document | 4v2f_full_validation.pdf.gz | 426.3 KB | Display | |
Data in XML | 4v2f_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 4v2f_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/4v2f ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2f | HTTPS FTP |
-Related structure data
Related structure data | 2xpuC 4d7mC 4d7nC 4v2gC 2tctS C: citing same article (ref.) S: Starting model for refinement |
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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: 23288.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PWH208 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: P0ACT4 |
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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: 2.38 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 8 / Details: PH 8.0 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9995 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9995 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30.8 Å / Num. obs: 7162 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.3 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2TCT Resolution: 2.4→65.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.991 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.674 / ESU R Free: 0.337 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.762 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→65.18 Å
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Refine LS restraints |
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