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Open data
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Basic information
Entry | Database: PDB / ID: 3chb | |||||||||
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Title | CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE | |||||||||
![]() | CHOLERA TOXIN | |||||||||
![]() | TOXIN / TOXIN-RECEPTOR COMPLEX / PENTASACCHARIDE | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Merritt, E.A. / Hol, W.G.J. | |||||||||
![]() | ![]() Title: The 1.25 A resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site. Authors: Merritt, E.A. / Kuhn, P. / Sarfaty, S. / Erbe, J.L. / Holmes, R.K. / Hol, W.G. #1: ![]() Title: Structural Studies of Receptor Binding by Cholera Toxin Mutants Authors: Merritt, E.A. / Sarfaty, S. / Jobling, M.G. / Chang, T. / Holmes, R.K. / Hirst, T.R. / Hol, W.G. #2: ![]() Title: Crystal Structure of Cholera Toxin B-Pentamer Bound to Receptor Gm1 Pentasaccharide Authors: Merritt, E.A. / Sarfaty, S. / Van Den Akker, F. / L'Hoir, C. / Martial, J.A. / Hol, W.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258 KB | Display | ![]() |
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PDB format | ![]() | 212.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 48.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2chbS S: Starting model for refinement |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.446207, -0.852405, -0.27259), Vector: |
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Components
-Protein , 1 types, 5 molecules DEFGH
#1: Protein | Mass: 11773.510 Da / Num. of mol.: 5 / Fragment: B-PENTAMER / Mutation: H94R Source method: isolated from a genetically manipulated source Details: RECEPTOR BINDING SITE ON EACH MONOMER OCCUPIED BY GM1 PENTASACCHARIDE Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 7 molecules ![](data/chem/img/GLC.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 3 types, 765 molecules ![](data/chem/img/UNX.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-UNX / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: SITTING DROP, pH 7.0, vapor diffusion - sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 125 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: BENT CRYSTAL + VERTICAL MIRROR |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→40 Å / Num. obs: 126728 / % possible obs: 92 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.25→1.3 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.4 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 858588 |
Reflection shell | *PLUS % possible obs: 84.4 % |
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Processing
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Refinement | Starting model: PDB ENTRY 2CHB Resolution: 1.25→22 Å / Num. parameters: 46849 / Num. restraintsaints: 21203 / Cross valid method: R-FREE / σ(F): 0 / Stereochemistry target values: SHELX-96
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Solvent computation | Solvent model: BABINET | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 12 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→22 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.18 / Rfactor Rwork: 0.1326 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |