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- PDB-1chp: SURPRISING LEADS FOR A CHOLERA TOXIN RECEPTOR BINDING ANTAGONIST;... -

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Basic information

Entry
Database: PDB / ID: 1chp
TitleSURPRISING LEADS FOR A CHOLERA TOXIN RECEPTOR BINDING ANTAGONIST; CRYSTALLOGRAPHIC STUDIES OF CTB MUTANTS
ComponentsCHOLERA TOXIN B PENTAMER
KeywordsTOXIN
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
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
Citation
Journal: Structure / Year: 1995
Title: Surprising leads for a cholera toxin receptor-binding antagonist: crystallographic studies of CTB mutants.
Authors: Merritt, E.A. / Sarfaty, S. / Chang, T.T. / Palmer, L.M. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.
#1: Journal: Protein Sci. / Year: 1994
Title: 2.2 Angstroms Crystal Structure of Cholera Toxin B5 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.J.
#2: Journal: Mol.Microbiol. / Year: 1991
Title: Analysis of Structure and Function of the B Subunit of Cholera Toxin by the Use of Site-Directed Mutagenesis
Authors: Jobling, M.G. / Holmes, R.K.
History
DepositionFeb 15, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET IN THE PENTAMER THE BETA SHEETS FROM ADJACENT MONOMERS COMBINE TO FORM A CONTINUOUS SIX- ...SHEET IN THE PENTAMER THE BETA SHEETS FROM ADJACENT MONOMERS COMBINE TO FORM A CONTINUOUS SIX-STRANDED ANTI-PARALLEL SHEET ACROSS EACH MONOMER-MONOMER INTERFACE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: CHOLERA TOXIN B PENTAMER
E: CHOLERA TOXIN B PENTAMER
F: CHOLERA TOXIN B PENTAMER
G: CHOLERA TOXIN B PENTAMER
H: CHOLERA TOXIN B PENTAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4426
Polymers58,4075
Non-polymers351
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-45 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.600, 66.610, 99.710
Angle α, β, γ (deg.)90.00, 131.57, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO D 93 / 2: CIS PROLINE - PRO E 93 / 3: CIS PROLINE - PRO F 93 / 4: CIS PROLINE - PRO G 93 / 5: CIS PROLINE - PRO H 93
DetailsCHOLERA TOXIN IS AN AB5 HEXAMER. THE B-PENTAMER OF CHOLERA TOXIN IS RESPONSIBLE FOR RECEPTOR RECOGNITION AND BINDING.

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Components

#1: Protein
CHOLERA TOXIN B PENTAMER / CHOLERAGEN


Mass: 11681.303 Da / Num. of mol.: 5 / Mutation: G33D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: OGAWA 41 (CLASSICAL) / Production host: Escherichia coli (E. coli) / References: UniProt: P01556
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FIVE IDENTICAL B SUBUNITS ARE LABELLED AS CHAINS D, E, F, G, AND H CORRESPONDING TO CHAIN ...THE FIVE IDENTICAL B SUBUNITS ARE LABELLED AS CHAINS D, E, F, G, AND H CORRESPONDING TO CHAIN IDENTIFIERS USED FOR THE RELATED HEAT-LABILE ENTEROTOXIN (LT) FROM ESCHERICHIA COLI AND FOR THE WILD TYPE CHOLERA TOXIN/RECEPTOR COMPLEX. SUBUNIT CHAIN RESIDUES B#1 D 1 - 103 B#2 E 1 - 103 B#3 F 1 - 103 B#4 G 1 - 103 B#5 H 1 - 103 WATER 1 - 248 CHLORIDE 249 - 249

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM1reservoirNaCl
2100 mMcacodylate1reservoir
310 mMimidazole1reservoir
4200 mM1reservoirMgCl2
516 %PEG10001reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Jul 14, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 32710 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2.85 % / Rmerge(I) obs: 0.081
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.081

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Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2→12 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.178 --
obs0.178 28286 83.3 %
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 1 248 4339
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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