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Yorodumi- PDB-1ysp: Crystal structure of the C-terminal domain of E. coli transcripti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ysp | ||||||
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Title | Crystal structure of the C-terminal domain of E. coli transcriptional regulator KdgR. | ||||||
Components | Transcriptional regulator kdgR | ||||||
Keywords | TRANSCRIPTION / transcriptional regulator / KdgR / IclR / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bochkarev, A. / Lunin, V.V. / Ezersky, A. / Evdokimova, E. / Skarina, T. / Xu, X. / Borek, D. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structural study of effector binding specificity in IclR transcriptional regulators Authors: Bochkarev, A. / Lunin, V.V. / Ezersky, A. / Evdokimova, E. / Skarina, T. / Xu, X. / Borek, D. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ysp.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ysp.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ysp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/1ysp ftp://data.pdbj.org/pub/pdb/validation_reports/ys/1ysp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20842.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdgR / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P76268 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.4 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG8K, 0.1M NaCacodylate, o.2M (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→76.7 Å / Num. all: 15893 / Num. obs: 15893 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.69→1.75 Å / % possible all: 10.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→76.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.237 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS DURING REFINEMENT
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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: 34.196 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→76.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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