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- PDB-1xtc: CHOLERA TOXIN -

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Basic information

Entry
Database: PDB / ID: 1xtc
TitleCHOLERA TOXIN
Components(CHOLERA TOXIN) x 3
KeywordsTOXIN / ENTEROTOXIN
Function / homology
Function and homology information


symbiont-mediated activation of host G protein-coupled receptor signal transduction / host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / nucleotidyltransferase activity / toxin activity / periplasmic space ...symbiont-mediated activation of host G protein-coupled receptor signal transduction / host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / nucleotidyltransferase activity / toxin activity / periplasmic space / lipid binding / host cell plasma membrane / extracellular space / extracellular region / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #240 / Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #240 / Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cholera enterotoxin subunit A / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsZhang, R.-G. / Westbrook, E.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The three-dimensional crystal structure of cholera toxin.
Authors: Zhang, R.G. / Scott, D.L. / Westbrook, M.L. / Nance, S. / Spangler, B.D. / Shipley, G.G. / Westbrook, E.M.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The 2.4 A Crystal Structure of Cholera Toxin B Subunit Pentamer: Choleragenoid
Authors: Zhang, R.G. / Westbrook, M.L. / Westbrook, E.M. / Scott, D.L. / Otwinowski, Z. / Maulik, P.R. / Reed, R.A. / Shipley, G.G.
History
DepositionJan 10, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHOLERA TOXIN
C: CHOLERA TOXIN
D: CHOLERA TOXIN
E: CHOLERA TOXIN
F: CHOLERA TOXIN
G: CHOLERA TOXIN
H: CHOLERA TOXIN


Theoretical massNumber of molelcules
Total (without water)85,7097
Polymers85,7097
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19330 Å2
ΔGint-67 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.000, 92.200, 60.600
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHOLERA TOXIN / CTX / CHOLERAGEN


Mass: 21841.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMMERCIALLY OBTAINED FROM LIST BIOLOGICAL LABORATORY, CAMPBER CA95008
Source: (natural) Vibrio cholerae (bacteria) / Strain: 569B / References: UniProt: P01555
#2: Protein/peptide CHOLERA TOXIN / CTX / CHOLERAGEN


Mass: 5404.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMMERCIALLY OBTAINED FROM LIST BIOLOGICAL LABORATORY, CAMPBER CA95008
Source: (natural) Vibrio cholerae (bacteria) / Strain: 569B / References: UniProt: P01555
#3: Protein
CHOLERA TOXIN / CTX / CHOLERAGEN


Mass: 11692.346 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: COMMERCIALLY OBTAINED FROM LIST BIOLOGICAL LABORATORY, CAMPBER CA95008
Source: (natural) Vibrio cholerae (bacteria) / Strain: 569B / References: UniProt: P01556
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHOLERA TOXIN CONTAINS 3 KINDS OF CHAINS: AN ALPHA AND A GAMMA CHAIN (FROM THE SAME PRECURSOR ...CHOLERA TOXIN CONTAINS 3 KINDS OF CHAINS: AN ALPHA AND A GAMMA CHAIN (FROM THE SAME PRECURSOR MOLECULE), LINKED BY AN INTERCHAIN DISULFIDE BOND, ASSOCIATED NONCOVALENTLY WITH AN AGGREGATE OF 4 TO 6 BETA CHAINS. CHAIN A IS THE A1 OR ALPHA CHAIN, CHAIN C IS THE A2 OR GAMMA CHAIN, AND CHAINS D, E, F, G, AND H ARE THE FIVE ASSOCIATED BETA CHAINS.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal grow
*PLUS
Method: other / Details: Spangler, B.D., (1989) Biochemistry, 28, 1333.

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Aug 15, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 26200 / % possible obs: 88.4 % / Rmerge(I) obs: 0.048
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 60810 / Rmerge(I) obs: 0.048

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Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementHighest resolution: 2.4 Å / σ(F): 1.5 /
RfactorNum. reflection
Rwork0.185 -
obs-26200
Displacement parametersBiso mean: 20.37 Å2
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5997 0 0 138 6135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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