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- PDB-1ltg: THE ARG7LYS MUTANT OF HEAT-LABILE ENTEROTOXIN EXHIBITS GREAT FLEX... -

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Basic information

Entry
Database: PDB / ID: 1ltg
TitleTHE ARG7LYS MUTANT OF HEAT-LABILE ENTEROTOXIN EXHIBITS GREAT FLEXIBILITY OF ACTIVE SITE LOOP 47-56 OF THE A SUBUNIT
Components(HEAT-LABILE ENTEROTOXIN) x 3
KeywordsENTEROTOXIN
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
Heat-labile enterotoxin A chain / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsVan Den Akker, F. / Hol, W.G.J.
Citation
Journal: Biochemistry / Year: 1995
Title: The Arg7Lys mutant of heat-labile enterotoxin exhibits great flexibility of active site loop 47-56 of the A subunit.
Authors: van den Akker, F. / Merritt, E.A. / Pizza, M. / Domenighini, 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.M. / Dauter, Z. / Kingma, J. / Witholt, B. / Hol, W.G.J.
#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.M. / Witholt, B. / Hol, W.G.J.
History
DepositionJun 13, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET IN THE PENTAMER THE BETA SHEETS FROM ADJACENT MONOMERS COMBINE TO FORM A CONTINUOUS SIX- ...SHEET IN THE PENTAMER THE BETA SHEETS FROM ADJACENT MONOMERS COMBINE TO FORM A CONTINUOUS SIX-STRANDED ANTI-PARALLEL SHEET ACROSS EACH MONOMER-MONOMER INTERFACE.

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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
C: HEAT-LABILE ENTEROTOXIN


Theoretical massNumber of molelcules
Total (without water)86,8797
Polymers86,8797
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19690 Å2
ΔGint-82 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.700, 98.500, 65.500
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
DetailsTHE ASYMMETRIC UNIT CONTAINS ONE AB5 TOXIN HEXAMER. THE A SUBUNIT CONTAINS TWO FRAGMENTS, CONVENTIONALLY REFERRED TO AS A1 AND A2, WHICH ARE LABELED AS CHAINS A AND C IN THIS COORDINATE SET.

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN / LT


Mass: 11807.539 Da / Num. of mol.: 5 / Mutation: ARG A 7 LYS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE ESCHERICHIA COLI / Variant: PLASMID EWD299 / Plasmid: BLUESCRIPT-KS VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: P32890
#2: Protein HEAT-LABILE ENTEROTOXIN / LT


Mass: 21901.086 Da / Num. of mol.: 1 / Mutation: ARG A 7 LYS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE ESCHERICHIA COLI / Variant: PLASMID EWD299 / Plasmid: BLUESCRIPT-KS VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: P06717
#3: Protein/peptide HEAT-LABILE ENTEROTOXIN / LT


Mass: 5940.504 Da / Num. of mol.: 1 / Mutation: ARG A 7 LYS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE ESCHERICHIA COLI / Variant: PLASMID EWD299 / Plasmid: BLUESCRIPT-KS VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: P06717
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE ARG 7 IN THE A SUBUNIT OF THE WILD TYPE TOXIN HAS BEEN MUTATED TO LYS IN THIS STRUCTURE.
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.2 mg/mlprotein11
218 mMNAD12
30.8 mMguanyltyramine12
4210 mM12NaCl
56.7 %PEG12

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Oct 31, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.073
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. obs: 22826 / % possible obs: 75 % / Observed criterion σ(F): 2 / Num. measured all: 60917 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.48 Å / % possible obs: 54 %

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Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.4→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.178 -
obs0.178 22826
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 0 71 5967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.99
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

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