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Yorodumi- PDB-5o8y: Conformational dynamism for DNA interaction in Salmonella typhimu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o8y | ||||||||||||
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Title | Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator. | ||||||||||||
Components | Transcriptional regulatory protein RcsB | ||||||||||||
Keywords | TRANSCRIPTION / Response regulator Transcriptional factor | ||||||||||||
Function / homology | Function and homology information phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Casino, P. / Marina, A. / Miguel-Romero, L. / Huesa, J. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Conformational dynamism for DNA interaction in the Salmonella RcsB response regulator. Authors: Casino, P. / Miguel-Romero, L. / Huesa, J. / Garcia, P. / Garcia-Del Portillo, F. / Marina, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o8y.cif.gz | 241.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o8y.ent.gz | 195.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/5o8y ftp://data.pdbj.org/pub/pdb/validation_reports/o8/5o8y | HTTPS FTP |
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-Related structure data
Related structure data | 5o8zC 6eo2C 6eo3C 1a04S 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
#1: Protein | Mass: 23743.650 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: rcsB, STM2270 / Production host: Escherichia coli (E. coli) / References: UniProt: P58663 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 3.19 Å3/Da / Density % sol: 61.39 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.4M lithium sulfate 8% PEG1000 Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.256→102.6 Å / Num. obs: 87626 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.035 / Rrim(I) all: 0.179 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.256→2.264 Å / Redundancy: 1.7 % / Num. unique obs: 845 / Rpim(I) all: 0.652 / Rrim(I) all: 2.958 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A04 Resolution: 2.3→102.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.777 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.206 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.366 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→102.56 Å
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Refine LS restraints |
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