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- PDB-5elf: Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide -

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Basic information

Entry
Database: PDB / ID: 5elf
TitleCholera toxin El Tor B-pentamer in complex with A-pentasaccharide
ComponentsCholera enterotoxin subunit B
KeywordsTOXIN / Cholera toxin B-pentamer / Human milk oligosaccharide / complex / blood group oligosaccharide/antigen
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
alpha-L-fucopyranose / alpha-D-glucopyranose / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHeggelund, J.E. / Burschowsky, D. / Krengel, U.
CitationJournal: Plos Pathog. / Year: 2016
Title: High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence.
Authors: Heggelund, J.E. / Burschowsky, D. / Bjrnestad, V.A. / Hodnik, V. / Anderluh, G. / Krengel, U.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_alt_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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: 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
A: Cholera enterotoxin subunit B
B: Cholera enterotoxin subunit B
C: Cholera enterotoxin subunit B
D: Cholera enterotoxin subunit B
E: Cholera enterotoxin subunit B
F: Cholera enterotoxin subunit B
G: Cholera enterotoxin subunit B
H: Cholera enterotoxin subunit B
I: Cholera enterotoxin subunit B
J: Cholera enterotoxin subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,38342
Polymers116,60310
Non-polymers8,78032
Water21,5101194
1
A: Cholera enterotoxin subunit B
B: Cholera enterotoxin subunit B
C: Cholera enterotoxin subunit B
D: Cholera enterotoxin subunit B
E: Cholera enterotoxin subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,19230
Polymers58,3025
Non-polymers4,89025
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Cholera enterotoxin subunit B
G: Cholera enterotoxin subunit B
H: Cholera enterotoxin subunit B
I: Cholera enterotoxin subunit B
J: Cholera enterotoxin subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,19112
Polymers58,3025
Non-polymers3,8907
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.626, 84.720, 195.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Cholera enterotoxin subunit B / Cholera enterotoxin B chain / Cholera enterotoxin gamma chain / Choleragenoid


Mass: 11660.348 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: ctxB, toxB, VC_1456 / Production host: Vibrio (bacteria) / Strain (production host): sp. 60 / References: UniProt: P01556

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Sugars , 4 types, 11 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 837.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-4[LFucpa1-3]DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1a_1-5][a1221m-1a_1-5][a2112h-1b_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-2-4/a3-b1_a4-c1_c2-d1_c3-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 837.771 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-4[LFucpa1-3]DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a1221m-1a_1-5][a2112h-1b_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-2-4/a3-b1_a4-c1_c2-d1_c3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: 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 , 4 types, 1215 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1194 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bicine-Tris, 9% PEG1000, 9% PEG3350, 9% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride. Microseeding.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→48.92 Å / Num. obs: 153547 / % possible obs: 99.6 % / Redundancy: 5.2 % / Net I/σ(I): 9.2
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSJanuary 10, 2014data reduction
XDSJanuary 10, 2014data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CHB

3chb


Resolution: 1.55→48.92 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.761 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21956 7664 5 %RANDOM
Rwork0.17907 ---
obs0.1811 145899 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.241 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2--2.12 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.55→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8170 0 554 1194 9918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.029171
X-RAY DIFFRACTIONr_bond_other_d0.0040.028775
X-RAY DIFFRACTIONr_angle_refined_deg1.9022.02912470
X-RAY DIFFRACTIONr_angle_other_deg1.2313.03520418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15451048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44625.416373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.505151586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.311530
X-RAY DIFFRACTIONr_chiral_restr0.1530.21585
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029515
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021873
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4791.7994147
X-RAY DIFFRACTIONr_mcbond_other1.4761.7984146
X-RAY DIFFRACTIONr_mcangle_it2.1782.6845177
X-RAY DIFFRACTIONr_mcangle_other2.1792.6855178
X-RAY DIFFRACTIONr_scbond_it2.0542.1035024
X-RAY DIFFRACTIONr_scbond_other2.0522.1035024
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.133.0717283
X-RAY DIFFRACTIONr_long_range_B_refined5.64116.58411232
X-RAY DIFFRACTIONr_long_range_B_other5.64216.58611233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.549→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 530 -
Rwork0.352 10549 -
obs--97.91 %

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