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Open data
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Basic information
Entry | Database: PDB / ID: 7vhf | ||||||
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Title | Crystal structure of the STX2a complexed with RRA peptide | ||||||
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![]() | TOXIN / Shiga Toxin | ||||||
Function / homology | ![]() hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / metabolic process / toxin activity / negative regulation of translation / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Senda, M. / Takahashi, M. / Nishikawa, K. / Senda, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin. Authors: Watanabe-Takahashi, M. / Senda, M. / Yoshino, R. / Hibino, M. / Hama, S. / Terada, T. / Shimizu, K. / Senda, T. / Nishikawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146 KB | Display | ![]() |
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PDB format | ![]() | 113.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.1 KB | Display | ![]() |
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Full document | ![]() | 480.6 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 40.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vhcC ![]() 7vhdC ![]() 7vheC ![]() 7d6rS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 33228.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 7824.590 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules G
#3: Protein/peptide | Mass: 401.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 434 molecules ![](data/chem/img/1PS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-1PS / #5: Chemical | ChemComp-GOL / | #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: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 4 M Sodium Formate, 100mM MES pH 6.5, 50 mM PPS |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 4, 2018 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→47.85 Å / Num. obs: 74551 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 15.42 Å2 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.75→1.78 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D6R Resolution: 1.75→47.85 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.826 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→47.85 Å
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Refine LS restraints |
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LS refinement shell |
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