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- PDB-6zix: Structure of RcsB from Salmonella enterica serovar Typhimurium bo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zix | |||||||||||||||
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Title | Structure of RcsB from Salmonella enterica serovar Typhimurium bound to promoter P1flhDC in the presence of phosphomimetic BeF3- | |||||||||||||||
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![]() | DNA BINDING PROTEIN / response regulator / phosphorylation / two-component systems / transcriptional factor | |||||||||||||||
Function / homology | ![]() phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Huesa, J. / Marina, A. / Casino, P. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon. Authors: Huesa, J. / Giner-Lamia, J. / Pucciarelli, M.G. / Paredes-Martinez, F. / Portillo, F.G. / Marina, A. / Casino, P. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.5 KB | Display | ![]() |
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PDB format | ![]() | 82.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 819.1 KB | Display | ![]() |
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Full document | ![]() | 824.1 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ziiC ![]() 6zilC ![]() 6zj2C ![]() 5o8zS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 23743.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rcsB, STM2270 / Production host: ![]() ![]() |
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-P1flhDC promoter sequence of 23 ... , 2 types, 2 molecules EF
#2: DNA chain | Mass: 7137.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A double-stranded DNA chain E: CGAATTAGGAAAAATCTTAGGCG chain F: GCTTAATCCTTTTTAGAATCCGC Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#3: DNA chain | Mass: 6981.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A double-stranded DNA chain E: CGAATTAGGAAAAATCTTAGGCG chain F: GCTTAATCCTTTTTAGAATCCGC Source: (gene. exp.) ![]() Production host: ![]() ![]() |
-Non-polymers , 3 types, 9 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.41 Å3/Da / Density % sol: 72.12 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 1.5M ammonium sulfate, 1.6% glycerol and 0.8M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.4→74.34 Å / Num. obs: 14477 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Net I/σ(I): 11.8 / Num. measured all: 69020 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5O8Z Resolution: 3.4→57.79 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.959 / SU B: 77.191 / SU ML: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 296.75 Å2 / Biso mean: 169.022 Å2 / Biso min: 73.91 Å2
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Refinement step | Cycle: final / Resolution: 3.4→57.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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