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- PDB-2chb: CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE -

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Basic information

Entry
Database: PDB / ID: 2chb
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 / 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 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
Citation
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.
#1: 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
DepositionJun 3, 1997Processing site: BNL
SupersessionDec 3, 1997ID: 1CHB
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)63,44210
Polymers58,7725
Non-polymers4,6705
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint23 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.900, 67.580, 80.470
Angle α, β, γ (deg.)90.00, 105.69, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.451348, -0.852471, -0.263775), (0.845821, 0.314495, 0.430906), (-0.284379, -0.417595, 0.862985)38.1221, 20.7847, 18.8104
2given(-0.451209, -0.536654, -0.713031), (0.521179, -0.807037, 0.277602), (-0.724419, -0.24636, 0.643835)32.3756, 67.899, 15.4226
3given(-0.448617, 0.509795, -0.734065), (-0.532801, -0.811995, -0.2383), (-0.717542, 0.284205, 0.635894)-8.985, 76.0536, -5.7737
4given(0.444061, 0.849074, -0.286151), (-0.854035, 0.304509, -0.421781), (-0.270988, 0.431679, 0.86036)-29.4784, 34.3008, -15.0119

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Components

#1: Protein
CHOLERA TOXIN


Mass: 11754.463 Da / Num. of mol.: 5 / Fragment: B-PENTAMER
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
#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
WURCS=2.0/3,4,3/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-1/a3-b2_a4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][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
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2/a4-b1_b3-c2_b4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.5 / Details: 200 MM MGCL2 100 MM CACODYLATE 5% PEG 1000 PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
210 mMHEPES1drop
31 mMGM11drop
4200 mM1reservoirMgCl2
515 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 35318 / % possible obs: 100 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2→2.25 Å / Rmerge(I) obs: 0.246 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
XENGENdata collection
MACROdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
MACROdata scaling
X-PLOR3.1phasing
RefinementStarting model: PDB ENTRY 1CHB

1chb
PDB Unreleased entry


Resolution: 2→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.171 --
obs0.171 28828 81.4 %
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--8.01 Å20 Å2-3.97 Å2
2--2.57 Å20 Å2
3---5.44 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 316 388 4774
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.73
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_it2.72
X-RAY DIFFRACTIONx_mcangle_it4.34
X-RAY DIFFRACTIONx_scbond_it2.72
X-RAY DIFFRACTIONx_scangle_it4.34
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rwork0.271 1863 -
obs--52.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM1.CHOTOPH1.CHO (MODIFIED)
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.271

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