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- PDB-1ltt: LACTOSE BINDING TO HEAT-LABILE ENTEROTOXIN REVEALED BY X-RAY CRYS... -

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Basic information

Entry
Database: PDB / ID: 1ltt
TitleLACTOSE BINDING TO HEAT-LABILE ENTEROTOXIN REVEALED BY X-RAY CRYSTALLOGRAPHY
Components
  • (HEAT-LABILE ENTEROTOXIN, SUBUNIT AHeat-labile enterotoxin family) x 2
  • HEAT-LABILE ENTEROTOXIN, SUBUNIT BHeat-labile enterotoxin family
KeywordsTOXIN
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
beta-lactose / Heat-labile enterotoxin A chain / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSixma, T.K. / Hol, W.G.J.
Citation
Journal: Nature / Year: 1992
Title: Lactose binding to heat-labile enterotoxin revealed by X-ray crystallography.
Authors: Sixma, T.K. / Pronk, S.E. / Kalk, K.H. / van Zanten, B.A. / Berghuis, A.M. / Hol, W.G.
#1: Journal: Nature / Year: 1991
Title: Crystal Structure of a Cholera Toxin-Related Heat-Labile Enterotoxin from E. Coli
Authors: Sixma, T.K. / Pronk, S.E. / Kalk, K.H. / Wartna, E.S. / Van Zanten, B.A.M. / Witholt, B. / Hol, W.G.J.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structure of E. Coli Heat Labile Enterotoxin, a Close Relative of Cholera Toxin
Authors: Sixma, T.K. / Van Zanten, B.A.M. / Dauter, Z. / Hol, W.G.J.
History
DepositionJul 15, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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 / 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 / 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 / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HEAT-LABILE ENTEROTOXIN, SUBUNIT B
E: HEAT-LABILE ENTEROTOXIN, SUBUNIT B
F: HEAT-LABILE ENTEROTOXIN, SUBUNIT B
G: HEAT-LABILE ENTEROTOXIN, SUBUNIT B
H: HEAT-LABILE ENTEROTOXIN, SUBUNIT B
A: HEAT-LABILE ENTEROTOXIN, SUBUNIT A
C: HEAT-LABILE ENTEROTOXIN, SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,05712
Polymers85,3467
Non-polymers1,7115
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.800, 101.200, 64.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO D 93 / 2: CIS PROLINE - PRO E 93 / 3: CIS PROLINE - PRO F 93 / 4: CIS PROLINE - PRO G 93 / 5: CIS PROLINE - PRO H 93 / 6: CIS PROLINE - PRO A 178
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.986307, 0.072994, -0.147886), (-0.163423, 0.312057, -0.935902), (-0.022166, 0.947255, 0.319713)1.547, 63.178, -21.273
2given(0.964145, -0.045324, -0.261478), (-0.191442, -0.80114, -0.567032), (-0.18378, 0.596759, -0.781092)10.832, 102.55, 31.741
3given(0.964145, -0.191441, -0.18378), (-0.045324, -0.80114, 0.596759), (-0.261477, -0.567032, -0.781092)15.022, 63.706, 85.774
4given(0.986308, -0.16342, -0.022164), (0.072991, 0.312057, 0.947255), (-0.147884, -0.935903, 0.319713)8.327, 0.323, 66.158
DetailsROTATION MATRICES HAVE BEEN INCLUDED FOR PARTIAL NON-CRYSTALLOGRAPHIC FIVEFOLD SYMMETRY OF THE B SUBUNITS. ROTATIONS ACT ON CARTESIAN COORDINATES, WITH THE ORIGIN AS CENTER OF ROTATION (NO TRANSLATION ALONG THE FIVEFOLD AXIS). RMS DEVIATION FOR ALL 515 ALPHA CARBONS OF THE B SUBUNIT IS 0.6 ANGSTROMS. (SUPERPOSITION OF INDIVIDUAL B SUBUNITS GIVES BETTER VALUES OF 0.20 - 0.45 ANGSTROMS). ROTATIONS IN POLAR COORDINATES: KAPPA PHI PSI RELATING 288.0 7.2 94.7 B1 TO B2 (MTRIX1) 216.0 7.2 94.7 B1 TO B3 (MTRIX2) 144.0 7.2 94.7 B1 TO B4 (MTRIX3) 72.0 7.2 94.7 B1 TO B5 (MTRIX4) THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *E* WHEN APPLIED TO CHAIN *D*. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *F* WHEN APPLIED TO CHAIN *D*. THE TRANSFORMATION PRESENTED AS *MTRIX 3* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *G* WHEN APPLIED TO CHAIN *D*. THE TRANSFORMATION PRESENTED AS *MTRIX 4* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *H* WHEN APPLIED TO CHAIN *D*.

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN, SUBUNIT B / Heat-labile enterotoxin family


Mass: 11807.539 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Organ: TAIL / Production host: Escherichia coli (E. coli) / References: UniProt: P32890
#2: Protein HEAT-LABILE ENTEROTOXIN, SUBUNIT A / Heat-labile enterotoxin family


Mass: 21354.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Organ: TAIL / Production host: Escherichia coli (E. coli) / References: UniProt: P06717
#3: Protein/peptide HEAT-LABILE ENTEROTOXIN, SUBUNIT A / Heat-labile enterotoxin family


Mass: 4953.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Organ: TAIL / Production host: Escherichia coli (E. coli) / References: UniProt: P06717
#4: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS THE UNNICKED AND UNREDUCED FORM OF THE TOXIN.
Sequence detailsSUBUNIT NUMBERING SCHEME: SUBUNIT CHAIN PROTEIN SEQUENCE B1 D 1 - 103 B2 E 1 - 103 B3 F 1 - 103 B4 ...SUBUNIT NUMBERING SCHEME: SUBUNIT CHAIN PROTEIN SEQUENCE B1 D 1 - 103 B2 E 1 - 103 B3 F 1 - 103 B4 G 1 - 103 B5 H 1 - 103 A1 A 1 - 188 A2 C 196 - 237 GALACTOSE D 104 GLUCOSE D 105 GALACTOSE E 104 GLUCOSE E 105 GALACTOSE F 104 GLUCOSE F 105 GALACTOSE G 104 GLUCOSE G 105 GALACTOSE H 104 GLUCOSE H 105 WATER 1 - 334

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Details: three-layer liquid-liquid diffusion, taken from Pronk, S.E. et al (1985). J. Biol. Chem., 260, 13580-13584.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl11
21 mMEDTA11
33 mM11NaN3
40.3 MKF11
525 mMlactose12
710 mg/mlprecipitant11
850 mMTris-HCl13
93 mMEDTA13
100.3 M13NaN3
1115 %PEG600013
612NaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 91 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→8 Å / Rfactor Rwork: 0.182 / Rfactor obs: 0.182
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 115 334 6427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Num. reflection obs: 5978 / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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