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Open data
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Basic information
Entry | Database: PDB / ID: 5ele | |||||||||
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Title | Cholera toxin El Tor B-pentamer in complex with A Lewis-y | |||||||||
![]() | Cholera enterotoxin subunit B | |||||||||
![]() | TOXIN / Cholera toxin B-pentamer / A Lewis-y / complex / blood group oligosaccharide/antigen | |||||||||
Function / homology | ![]() host cell surface binding / galactose binding / catalytic complex / positive regulation of tyrosine phosphorylation of STAT protein / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Heggelund, J.E. / Burschowsky, D. / Krengel, U. | |||||||||
![]() | ![]() Title: High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence. Authors: Heggelund, J.E. / Burschowsky, D. / Bjrnestad, V.A. / Hodnik, V. / Anderluh, G. / Krengel, U. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.9 KB | Display | ![]() |
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PDB format | ![]() | 201.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 53.9 KB | Display | |
Data in CIF | ![]() | 75.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5elbC ![]() 5elcC ![]() 5eldC ![]() 5elfC ![]() 3chbS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 11660.348 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 8 molecules ![](data/chem/img/FUC.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#2: Polysaccharide | #4: Sugar | ChemComp-FUC / #7: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 971 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #5: Chemical | ChemComp-BCN / #6: Chemical | ChemComp-1PE / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Bicine-Tris, 9% PEG1000, 9% PEG3350, 9% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→49.14 Å / Num. obs: 136523 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 0.49 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CHB Resolution: 1.6→49.14 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.065 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.341 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→49.14 Å
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Refine LS restraints |
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