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- PDB-1lt5: HEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH THIODIGALACTOSIDE -

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Basic information

Entry
Database: PDB / ID: 1lt5
TitleHEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH THIODIGALACTOSIDE
ComponentsHEAT-LABILE ENTEROTOXIN
KeywordsENTEROTOXIN
Function / homology
Function and homology information


toxin activity / killing of cells of another organism / extracellular region
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
thiodigalactoside / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
Citation
Journal: Structure / Year: 1997
Title: Structural foundation for the design of receptor antagonists targeting Escherichia coli heat-labile enterotoxin.
Authors: Merritt, E.A. / Sarfaty, S. / Feil, I.K. / Hol, W.G.
#1: Journal: Mol.Microbiol. / Year: 1994
Title: Galactose-Binding Site in Escherichia Coli Heat-Labile Enterotoxin (Lt) and Cholera Toxin (Ct)
Authors: Merritt, E.A. / Sixma, T.K. / Kalk, K.H. / Van Zanten, B.A. / Hol, W.G.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structure of Escherichia Coli Heat-Labile Enterotoxin, a Close Relative of Cholera Toxin
Authors: Sixma, T.K. / Kalk, K.H. / Van Zanten, B.A. / Dauter, Z. / Kingma, J. / Witholt, B. / Hol, W.G.
History
DepositionSep 30, 1997Processing site: BNL
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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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 / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 12, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_branch_scheme / pdbx_molecule_features / struct_conn
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 / _chem_comp.pdbx_synonyms / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.pdb_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id
Revision 3.1Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _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: HEAT-LABILE ENTEROTOXIN
E: HEAT-LABILE ENTEROTOXIN
F: HEAT-LABILE ENTEROTOXIN
G: HEAT-LABILE ENTEROTOXIN
H: HEAT-LABILE ENTEROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,83010
Polymers59,0385
Non-polymers1,7925
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-60 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.680, 100.130, 63.670
Angle α, β, γ (deg.)90.00, 107.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11807.539 Da / Num. of mol.: 5 / Fragment: B-PENTAMER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32890
#2: Polysaccharide
beta-D-galactopyranose-(1-1)-1-thio-beta-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 358.362 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides, and with reducing-end-to-reducing-end glycosidic bond
References: thiodigalactoside
DescriptorTypeProgram
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Galp1SH]{[(1+S)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: batch method / Details: three-layered solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
2100 mMTris-HCl11
3200 mM11NaCl
40.5 mMEDTA11
50.1 mMazide11
6200 mMthiodigalactoside12
7100 mMTris-HCl12
842 %PEG600013
9100 mMTris-HCl13
1protein11
1050 mM13NaCl

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.75
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: DOUBLY-FOCUSED MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 43351 / % possible obs: 77 % / Observed criterion σ(I): 0 / Redundancy: 2.86 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.5 / % possible all: 81
Reflection shell
*PLUS
% possible obs: 81 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTA

1lta


Resolution: 1.7→25 Å / σ(F): 1 / Details: BABINET BULK SOLVENT MODEL
RfactorNum. reflection% reflection
Rwork0.172 --
obs0.172 40978 73 %
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1-3.638 Å20 Å2-0.832 Å2
2--0.077 Å20 Å2
3----3.715 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 115 415 4650
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.922
X-RAY DIFFRACTIONx_mcangle_it3.174
X-RAY DIFFRACTIONx_scbond_it1.922
X-RAY DIFFRACTIONx_scangle_it3.174
LS refinement shellResolution: 1.7→1.72 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rwork0.2213 1551
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM1.CHOLOCALLY MODIFIED TOPH1.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34
LS refinement shell
*PLUS
Rfactor obs: 0.2213

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