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

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Basic information

Entry
Database: PDB / ID: 1chq
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 / positive regulation of tyrosine phosphorylation of STAT protein / catalytic complex / 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: 2.1 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 1.3Feb 12, 2014Group: Refinement description
Revision 1.4Jun 21, 2017Group: Refinement description / Category: software / Item: _software.version
Revision 1.5Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
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


Theoretical massNumber of molelcules
Total (without water)57,9065
Polymers57,9065
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-53 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.600, 67.390, 98.810
Angle α, β, γ (deg.)90.00, 131.63, 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: 11581.161 Da / Num. of mol.: 5 / Mutation: R35D
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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 - 105
Has protein modificationY
Nonpolymer detailsSOLVENT SITE 60 IS ALMOST CERTAINLY A CHLORIDE ION, AS ESTABLISHED FOR THE ISOMORPHOUS G33D MUTANT ...SOLVENT SITE 60 IS ALMOST CERTAINLY A CHLORIDE ION, AS ESTABLISHED FOR THE ISOMORPHOUS G33D MUTANT (PDB ENTRY 1CHP).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growpH: 6.4 / Details: pH 6.4
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMsialic acid1reservoir
2100 mMcacodylate1reservoir
310 mMHEPES1reservoir
4200 mM1reservoirMgCl2
513 %PEG10001reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Nov 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 28288 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 2.02 % / Rmerge(I) obs: 0.053
Reflection
*PLUS
Highest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
XENGEN3.1data collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.1→12 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.208 --
obs-22154 75.5 %
Displacement parametersBiso mean: 41.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 0 105 4115
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.81
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
Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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