+Open data
-Basic information
Entry | Database: PDB / ID: 3n6t | ||||||
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Title | Effector binding domain of TsaR | ||||||
Components | LysR type regulator of tsaMBCD | ||||||
Keywords | TRANSCRIPTION REGULATOR / Rossmann fold | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Comamonas testosteroni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Monferrer, D. / Uson, I. | ||||||
Citation | Journal: To be Published Title: Structural studies on the effector binding domain of TsaR Authors: Monferrer, D. / Perillo, M. / Sola, M. / Uson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n6t.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n6t.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 3n6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n6t_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 3n6t_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 3n6t_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3n6t_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/3n6t ftp://data.pdbj.org/pub/pdb/validation_reports/n6/3n6t | HTTPS FTP |
-Related structure data
Related structure data | 3n6uC 3fxqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22369.703 Da / Num. of mol.: 1 / Fragment: Effector binding domain, UNP residues 91-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: T-2 / Gene: tsa, tsaR / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P94678 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-ACT / | #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: 2.27 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.5M ammonium sulfate, 0.1M sodium acetate pH4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9785 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→41.53 Å / Num. obs: 19168 / % possible obs: 99.6 % / Redundancy: 1.83 % / Rmerge(I) obs: 0.059 / Rsym value: 0.0387 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 1.77 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.68 / Rsym value: 0.232 / % possible all: 97.9 |
-Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FXQ Resolution: 1.85→31.2 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.889 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R Free: 0.165 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.836 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→31.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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