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- PDB-1ltb: 2.6 ANGSTROMS CRYSTAL STRUCTURE OF PARTIALLY-ACTIVATED E. COLI HE... -

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Basic information

Entry
Database: PDB / ID: 1ltb
Title2.6 ANGSTROMS CRYSTAL STRUCTURE OF PARTIALLY-ACTIVATED E. COLI HEAT-LABILE ENTEROTOXIN (LT)
Components
  • (HEAT-LABILE ENTEROTOXIN, SUBUNIT A) x 2
  • HEAT-LABILE ENTEROTOXIN, SUBUNIT B
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: 2.6 Å
AuthorsMerritt, E.A. / Sixma, T.K. / Hol, W.G.J.
Citation
Journal: FEBS Lett. / Year: 1994
Title: Structure of partially-activated E. coli heat-labile enterotoxin (LT) at 2.6 A resolution.
Authors: Merritt, E.A. / Pronk, S.E. / Sixma, T.K. / Kalk, K.H. / van Zanten, B.A. / Hol, W.G.
#1: 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.
#2: 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
DepositionSep 15, 1993Processing 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 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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, 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


Theoretical massNumber of molelcules
Total (without water)85,8187
Polymers85,8187
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19780 Å2
ΔGint-76 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.200, 98.200, 64.800
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

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN, SUBUNIT B


Mass: 11807.539 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: EWD299 / Production host: Escherichia coli (E. coli) / References: UniProt: P32890
#2: Protein HEAT-LABILE ENTEROTOXIN, SUBUNIT A


Mass: 21354.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: EWD299 / Production host: Escherichia coli (E. coli) / References: UniProt: P06717
#3: Protein/peptide HEAT-LABILE ENTEROTOXIN, SUBUNIT A


Mass: 5425.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: EWD299 / Production host: Escherichia coli (E. coli) / References: UniProt: P06717
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS THE NICKED, UNREDUCED, FORM OF THE TOXIN. THE A AND C CHAINS ARE LINKED BY A DISULFIDE ...THIS IS THE NICKED, UNREDUCED, FORM OF THE TOXIN. THE A AND C CHAINS ARE LINKED BY A DISULFIDE BRIDGE BETWEEN A 187 AND C 199, BUT THE MAIN CHAIN BETWEEN THEM HAS BEEN TRYPSIN-CLEAVED. THE MODEL IS INCOMPLETE IN THE REGION OF THE CLEAVAGE SITE (189 - 195) DUE TO POOR ELECTRON DENSITY.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Details: two-layer method, 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
510 mg/mlprecipitant11
650 mMTris-HCl12
71 mMEDTA12
83 mM12NaN3
915 %PEG600012

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 21707 / % possible obs: 90 % / Num. measured all: 47662 / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.172 / Rfactor obs: 0.172 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 0 197 6175
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_deg3.24
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
Lowest resolution: 10 Å / Num. reflection all: 21320 / σ(I): 0 / Rfactor all: 0.172 / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.24

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