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- PDB-1lt4: HEAT-LABILE ENTEROTOXIN MUTANT S63K -

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Basic information

Entry
Database: PDB / ID: 1lt4
TitleHEAT-LABILE ENTEROTOXIN MUTANT S63K
Components(HEAT-LABILE ENTEROTOXIN) x 2
KeywordsENTEROTOXIN
Function / homology
Function and homology information


: / toxin activity / killing of cells of another organism / extracellular space / extracellular region
Similarity search - Function
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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex ...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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-lactose / Heat-labile enterotoxin A chain / Heat-labile enterotoxin B chain / Non toxic mutant of heat labile enterotoxin A subunit precursot
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / ISOMORPHOUS MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVan Den Akker, F. / Hol, W.G.J.
Citation
Journal: Protein Sci. / Year: 1997
Title: Crystal structure of a non-toxic mutant of heat-labile enterotoxin, which is a potent mucosal adjuvant.
Authors: van den Akker, F. / Pizza, M. / Rappuoli, R. / Hol, W.G.
#1: Journal: Mol.Microbiol. / Year: 1994
Title: Probing the Structure-Activity Relationship of Escherichia Coli Lt-A by Site-Directed Mutagenesis
Authors: Pizza, M. / Domenighini, M. / Hol, W. / Giannelli, V. / Fontana, M.R. / Giuliani, M.M. / Magagnoli, C. / Peppoloni, S. / Manetti, R. / Rappuoli, R.
#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.
#3: 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. / Witholt, B. / Hol, W.G.
History
DepositionApr 14, 1997Processing site: BNL
Revision 1.0Jun 16, 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 / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
A: HEAT-LABILE ENTEROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,40411
Polymers87,6926
Non-polymers1,7115
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.000, 101.900, 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. FRAGMENTS A1 AND A2 ARE COVALENTLY LINKED IN THE LATENT TOXIN AND ARE PROTEOLYTICALLY CLEAVED UPON ACTIVATION.

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Components

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


Mass: 11807.539 Da / Num. of mol.: 5 / Fragment: HOLOTOXIN / Mutation: CHAIN A, S63K
Source method: isolated from a genetically manipulated source
Details: LACTOSE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE / Production host: Escherichia coli (E. coli) / References: UniProt: P32890
#2: Protein HEAT-LABILE ENTEROTOXIN / LT-I


Mass: 28654.523 Da / Num. of mol.: 1 / Fragment: HOLOTOXIN / Mutation: CHAIN A, S63K
Source method: isolated from a genetically manipulated source
Details: LACTOSE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE / Production host: Escherichia coli (E. coli) / References: UniProt: P06717, UniProt: Q2HQJ7*PLUS
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Description: NO MOLECULAR REPLACEMENT SEARCH NEEDED TO BE PERFORMED BECAUSE THE SPACE GROUP AND CELL DIMENSIONS WERE IDENTICAL TO THE STARTING 1LTT STRUCTURE.
Crystal growMethod: 3 layer capillary method / pH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 5% PEG 6000, 100 MM NACL, 1 MM EDTA, 75 MM LACTOSE, 100 MM TRIS PH 7.5 USING THE 3 LAYER CAPPILARY METHOD, 3 layer capillary method
Crystal grow
*PLUS
Method: three-layer capillary
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlLT-I Ser63Lys11
25.6 %PEG600011
3100 mMTris11
4100 mM11NaCl
50.02 %11NaN3
675 mMlactose11

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 50516 / % possible obs: 93.3 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rsym value: 0.064 / Net I/σ(I): 18
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 5.1 / Rsym value: 0.156 / % possible all: 80
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 81.4 % / Rmerge(I) obs: 0.156

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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: ISOMORPHOUS MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTT

1ltt


Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES A 1 - A 3, A 189 - A 195, AND A 237 - A 240 ARE OMITTED FROM THE STRUCTURE BECAUSE OF POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2522 4.7 %RANDOM
Rwork0.192 ---
obs0.192 49792 92.9 %-
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5981 0 115 356 6452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
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
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.335 208 3.9 %
Rwork0.278 47270 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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