+Open data
-Basic information
Entry | Database: PDB / ID: 6hmy | |||||||||
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Title | Cholera toxin classical B-pentamer in complex with fucosyl-GM1 | |||||||||
Components | Cholera enterotoxin B-subunit | |||||||||
Keywords | TOXIN / cholera toxin / lectin / complex / fucosyl-GM1 / protein-carbohydrate interactions / X-ray crystal structure | |||||||||
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 / metal ion binding Similarity search - Function | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Krengel, U. / Heim, J.B. | |||||||||
Funding support | Norway, 1items
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Citation | Journal: Sci Rep / Year: 2019 Title: Crystal structures of cholera toxin in complex with fucosylated receptors point to importance of secondary binding site. Authors: Heim, J.B. / Hodnik, V. / Heggelund, J.E. / Anderluh, G. / Krengel, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hmy.cif.gz | 501.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hmy.ent.gz | 425.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hmy_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
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Full document | 6hmy_full_validation.pdf.gz | 4.9 MB | Display | |
Data in XML | 6hmy_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 6hmy_validation.cif.gz | 78.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/6hmy ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hmy | HTTPS FTP |
-Related structure data
Related structure data | 6hjdC 6hmwC 5elbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 11623.267 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: ctxB, C9J66_18955, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57193, UniProt: P01556*PLUS |
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-Sugars , 4 types, 12 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | |
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-Non-polymers , 3 types, 817 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-BCN / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.56 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 0.1 M Bicine-Tris, 6% PEG1000, 6% PEG3350, 6% 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: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.980802 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980802 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→44.32 Å / Num. obs: 150674 / % possible obs: 98.4 % / Redundancy: 2.6 % / Rrim(I) all: 0.176 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.6→1.63 Å / CC1/2: 0.449 / Rrim(I) all: 0.964 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ELB Resolution: 1.6→44.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.397 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / 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: 13.369 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→44.32 Å
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