+Open data
-Basic information
Entry | Database: PDB / ID: 6hmw | ||||||
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Title | Cholera toxin classical B-pentamer in complex with fucose | ||||||
Components | Cholera enterotoxin B-subunit | ||||||
Keywords | TOXIN / cholera toxin / lectin / complex / fucose / 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: 1.95 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 | 6hmw.cif.gz | 423.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hmw.ent.gz | 351.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hmw_validation.pdf.gz | 4.7 MB | Display | wwPDB validaton report |
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Full document | 6hmw_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 6hmw_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 6hmw_validation.cif.gz | 57.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/6hmw ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hmw | HTTPS FTP |
-Related structure data
Related structure data | 6hjdC 6hmyC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#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 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-BCN / #4: Sugar | ChemComp-FUL / #5: 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: 2.08 Å3/Da / Density % sol: 40.73 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 0.1 M Bicine-Tris, 10% PEG1000, 10% PEG3350, 10% 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: 0.979531 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979531 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→47.42 Å / Num. all: 184186 / Num. obs: 67464 / % possible obs: 97.7 % / Redundancy: 2.7 % / Rrim(I) all: 0.149 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 4577 / CC1/2: 0.41 / Rrim(I) all: 1.251 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ELB Resolution: 1.95→47.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.253 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.176 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.418 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→47.42 Å
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Refine LS restraints |
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