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- PDB-1lti: HEAT-LABILE ENTEROTOXIN (LT-I) COMPLEX WITH T-ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 1lti
TitleHEAT-LABILE ENTEROTOXIN (LT-I) COMPLEX WITH T-ANTIGEN
Components(HEAT LABILE ENTEROTOXIN TYPE ...) x 3
KeywordsENTEROTOXIN / ADP-RIBOSYL TRANSFERASE
Function / homology
Function and homology information


toxin activity / killing of cells of another organism / extracellular space / extracellular region
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
Thomsen-Friedenreich antigen / beta-D-galactopyranose / Heat-labile enterotoxin A chain / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.13 Å
AuthorsVan Den Akker, F. / Hol, W.G.J.
CitationJournal: Protein Sci. / Year: 1996
Title: Tumor marker disaccharide D-Gal-beta 1, 3-GalNAc complexed to heat-labile enterotoxin from Escherichia coli.
Authors: van den Akker, F. / Steensma, E. / Hol, W.G.
History
DepositionMay 9, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: 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 / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
D: HEAT LABILE ENTEROTOXIN TYPE I
E: HEAT LABILE ENTEROTOXIN TYPE I
F: HEAT LABILE ENTEROTOXIN TYPE I
G: HEAT LABILE ENTEROTOXIN TYPE I
H: HEAT LABILE ENTEROTOXIN TYPE I
A: HEAT LABILE ENTEROTOXIN TYPE I
C: HEAT LABILE ENTEROTOXIN TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,83111
Polymers86,9077
Non-polymers9244
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.700, 100.500, 64.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ASYMMETRIC UNIT CONTAINS ONE AB5 TOXIN HEXAMER. THE A SUBUNIT CONTAINS TWO FRAGMENTS LINKED BY A DISORDERED LOOP. THESE 2 FRAGMENTS ARE CONVENTIONALLY REFERRED TO AS A1 AND A2, WHICH ARE LABELED AS CHAINS A AND C IN THIS COORDINATE SET. FRAGMENT A1 AND A2 ARE COVALENTLY LINKED IN THE LATENT TOXIN AND ARE PROTEOLYTICALLY CLEAVED UPON ACTIVATION.

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Components

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HEAT LABILE ENTEROTOXIN TYPE ... , 3 types, 7 molecules DEFGHAC

#1: Protein
HEAT LABILE ENTEROTOXIN TYPE I / LT-I


Mass: 11807.539 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: LATENT/INACTIVE FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE ENTEROTOXIGENIC K12 / Plasmid: EWD299 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P32890
#2: Protein HEAT LABILE ENTEROTOXIN TYPE I / LT-I


Mass: 22086.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LATENT/INACTIVE FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE ENTEROTOXIGENIC K12 / Plasmid: EWD299 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P06717
#3: Protein/peptide HEAT LABILE ENTEROTOXIN TYPE I / LT-I


Mass: 5783.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LATENT/INACTIVE FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE ENTEROTOXIGENIC K12 / Plasmid: EWD299 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P06717

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Sugars , 2 types, 4 molecules

#4: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 183 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsD-GALACTOSE-BETA1,3-N-ACETYL-GALACTOSAMINE (GAL-BETA1, 3GALNAC) IS THE DISACCHARIDE PART OF THE ...D-GALACTOSE-BETA1,3-N-ACETYL-GALACTOSAMINE (GAL-BETA1, 3GALNAC) IS THE DISACCHARIDE PART OF THE THOMSEN FRIEDENREICH TUMOR ANTIGEN, OR T-ANTIGEN (D-GAL-BETA1, 3GALNAC-ALPHA-SER/THR). THE T-ANTIGEN IS ALSO THE TERMINAL DISACCHARIDE IN THE NATURAL GM1 (GAL-BETA1, 3GALNAC-BETA1-(NEU5AC-ALPHA2,3)-4-GAL-BETA1,4GLC-CERAMIDE) GANGLIOSIDE RECEPTOR FOR THE TOXIN.
Sequence detailsSUBUNIT NUMBERING SCHEME: SUBUNIT CHAIN PROTEIN SEQUENCE A1 A 4 - 188 A2 C 196 - 236 B#1 D 1 - 103 ...SUBUNIT NUMBERING SCHEME: SUBUNIT CHAIN PROTEIN SEQUENCE A1 A 4 - 188 A2 C 196 - 236 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 W 1 - 183 GALACTOSE D 104 GALACTOSE E 104 GALACTOSE G 104 N-ACETYL GALACTOSAMINE G 105 GALACTOSE H 104

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growMethod: liquid - liquid diffusion / pH: 7.5
Details: LIQUID-LIQUID DIFFUSION CAPILLARY CONTAINS: 0.1M TRIS PH 7.5, 0.1M NACL, 0.001M EDTA, 0.02% SODIUM AZIDE, 4.5 MG/ML LT-I, 0.025M LACTOSE AND 5% PEG 6000. CRYSTAL WAS SOAKED FOR 1 DAY IN ...Details: LIQUID-LIQUID DIFFUSION CAPILLARY CONTAINS: 0.1M TRIS PH 7.5, 0.1M NACL, 0.001M EDTA, 0.02% SODIUM AZIDE, 4.5 MG/ML LT-I, 0.025M LACTOSE AND 5% PEG 6000. CRYSTAL WAS SOAKED FOR 1 DAY IN LACTOSE FREE MOTHER LIQUOR CONTAINING 0.1M D-GAL-BETA1,3GALNAC BEFORE DATA COLLECTION., liquid - liquid diffusion
Crystal
*PLUS
Crystal grow
*PLUS
Method: three-layer capillary
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlLT11
2100 mMTris11
3200 mM11NaCl
41 mMEDTA11
50.02 %11NaN3
6166 mMlactose12
7100 mMTris12
814 %PEG600013
9100 mMTris13

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 10, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→77 Å / Num. obs: 38264 / % possible obs: 86.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.2
Reflection shellResolution: 2.13→2.25 Å / Rmerge(I) obs: 0.16 / % possible all: 73.5

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Processing

Software
NameVersionClassification
RAXISSOFTWAREdata collection
RAXISSOFTWAREdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.13→8 Å / Cross valid method: FREE-R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 -5 %RANDOM
Rwork0.185 ---
obs0.185 37447 86.5 %-
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 2.13→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 59 183 6220
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.96
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 36311 / Num. reflection Rfree: 1932
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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