+Open data
-Basic information
Entry | Database: PDB / ID: 5elc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cholera toxin El Tor B-pentamer in complex with Lewis-y | |||||||||
Components | Cholera enterotoxin subunit B | |||||||||
Keywords | TOXIN / Cholera toxin B-pentamer / Lewis-y / complex / blood group oligosaccharide/antigen | |||||||||
Function / homology | Function and homology information 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 | Vibrio cholerae O1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Heggelund, J.E. / Burschowsky, D. / Krengel, U. | |||||||||
Citation | Journal: Plos Pathog. / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5elc.cif.gz | 241.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5elc.ent.gz | 197.9 KB | Display | PDB format |
PDBx/mmJSON format | 5elc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5elc_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5elc_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 5elc_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 5elc_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/5elc ftp://data.pdbj.org/pub/pdb/validation_reports/el/5elc | HTTPS FTP |
-Related structure data
Related structure data | 5elbC 5eldC 5eleC 5elfC 3chbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Vibrio cholerae O1 (bacteria) / Gene: ctxB, toxB, VC_1456 / Production host: Vibrio (bacteria) / Strain (production host): Sp. 60 / References: UniProt: P01556 |
---|
-Sugars , 4 types, 10 molecules
#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 | Source method: isolated from a genetically manipulated source #4: Polysaccharide | #7: Sugar | ChemComp-FUC / | |
---|
-Non-polymers , 3 types, 674 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-BCN / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Bicine-Tris, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.62 Å / Num. obs: 146071 / % possible obs: 94.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.34 / % possible all: 85.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CHB Resolution: 1.5→47.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.539 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.088 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→47.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|