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- PDB-5o8z: Conformational dynamism for DNA interaction in Salmonella typhimu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o8z | ||||||||||||
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Title | Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator. | ||||||||||||
![]() | Transcriptional regulatory protein RcsB | ||||||||||||
![]() | TRANSCRIPTION / Response regulator Transcriptional factor | ||||||||||||
Function / homology | ![]() phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Casino, P. / Marina, A. / Miguel-Romero, L. / Huesa, J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.3 KB | Display | ![]() |
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PDB format | ![]() | 128.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.3 KB | Display | ![]() |
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Full document | ![]() | 439.2 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o8yC ![]() 6eo2C ![]() 6eo3C ![]() 1a04S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23743.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: rcsB, STM2270 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 29% Jeffamine ED2003 0.1M lithium sulfate Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.69 Å / Num. obs: 21487 / % possible obs: 97.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.851 / Num. unique obs: 1736 / Rpim(I) all: 0.37 / Rrim(I) all: 1.004 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A04 Resolution: 2.1→48.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.275 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.224 / 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: 47.953 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→48.69 Å
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Refine LS restraints |
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