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Open data
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Basic information
Entry | Database: PDB / ID: 5elb | |||||||||
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Title | Cholera toxin classical B-pentamer in complex with Lewis-y | |||||||||
![]() | Cholera enterotoxin B subunit | |||||||||
![]() | TOXIN / Cholera toxin B-pentamer / Lewis-y / complex / blood group oligosaccharide/antigen | |||||||||
Function / homology | ![]() | |||||||||
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 | ![]() | 560.8 KB | Display | ![]() |
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PDB format | ![]() | 471.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5 MB | Display | ![]() |
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Full document | ![]() | 5 MB | Display | |
Data in XML | ![]() | 68.2 KB | Display | |
Data in CIF | ![]() | 98 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5elcC ![]() 5eldC ![]() 5eleC ![]() 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 11623.267 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ctxB, EN12_07055, ERS013160_03498, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244, ERS013212_03447 Production host: ![]() ![]() |
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-Sugars , 4 types, 30 molecules ![](data/chem/img/GAL.gif)
![](data/chem/img/GLA.gif)
![](data/chem/img/GLA.gif)
#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis Y antigen / alpha anomer #3: Polysaccharide | Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-GAL / #6: Sugar | ChemComp-GLA / |
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-Non-polymers , 4 types, 1571 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #7: Chemical | ChemComp-BCN / #8: Chemical | ChemComp-PEG / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Bicine-Tris, 10% PEG1000, 10% PEG3350, 10% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride. Microseeding. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 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: 1.08→49.5 Å / Num. obs: 369957 / % possible obs: 78.9 % / Redundancy: 5.7 % / Net I/σ(I): 12.48 |
Reflection shell | Resolution: 1.08→1.14 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1 / % possible all: 19.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CHB Resolution: 1.08→49.49 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.311 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / 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: 14.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.08→49.49 Å
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Refine LS restraints |
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