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- PDB-3chb: CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE -

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Basic information

Entry
Database: PDB / ID: 3chb
TitleCHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE
ComponentsCHOLERA TOXIN
KeywordsTOXIN / TOXIN-RECEPTOR COMPLEX / PENTASACCHARIDE
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
alpha-D-glucopyranose / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
Citation
Journal: J.Mol.Biol. / Year: 1998
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: Journal: Protein Sci. / Year: 1997
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: Journal: Protein Sci. / Year: 1994
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
DepositionMar 24, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,28819
Polymers58,8685
Non-polymers5,42114
Water13,655758
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21490 Å2
ΔGint19 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.124, 66.176, 78.221
Angle α, β, γ (deg.)90.00, 106.33, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.446207, -0.852405, -0.27259), (0.85284, 0.312704, 0.418186), (-0.271223, -0.419073, 0.866496)
Vector: 37.8998, 21.8212, 18.6237)

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Components

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Protein , 1 types, 5 molecules DEFGH

#1: Protein
CHOLERA TOXIN


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.) Vibrio cholerae (bacteria) / Strain: OGAWA 41 (CLASSICAL BIOTYPE) / Production host: Escherichia coli (E. coli) / References: UniProt: P01556

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Sugars , 3 types, 7 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
[][D-1-deoxy-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 765 molecules

#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.4 %
Crystal growMethod: 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
IDConc.Common nameCrystal-IDSol-ID
110 mMHEPES1drop
20.001 mMPMSF1drop
30.001 mMleupeptin1drop
40.001 mMpepstain1drop
50.001 mMEDTA1drop
60.01 mMGM1 pentasaccharide1drop
722 %(w/v)PEG80001reservoir
810 %(w/v)mPEG3501reservoir
9200 mMcalcium acetate1reservoir
10100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: BENT CRYSTAL + VERTICAL MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELX-96refinement
CCP4(SCALA)data scaling
RefinementStarting model: PDB ENTRY 2CHB

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
RfactorNum. reflection% reflectionSelection details
Rfree0.18 6491 5 %RANDOM
all0.1326 123337 --
obs0.1326 -92 %-
Solvent computationSolvent model: BABINET
Refine analyzeNum. disordered residues: 12
Refinement stepCycle: LAST / Resolution: 1.25→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 347 758 5203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0.016
X-RAY DIFFRACTIONs_from_restr_planes0.423
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.07
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.046
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.18 / Rfactor Rwork: 0.1326
Solvent computation
*PLUS
Displacement parameters
*PLUS

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