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- PDB-1tii: ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB -

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Basic information

Entry
Database: PDB / ID: 1tii
TitleESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB
Components(HEAT LABILE ENTEROTOXIN TYPE IIB) x 3
KeywordsENTEROTOXIN / ADP-RIBOSYL TRANSFERASE / ADP-RIBOSYLATION / GANGLIOSIDE RECEPTOR
Function / homology
Function and homology information


host cell membrane / toxin activity / molecular adaptor activity / extracellular space / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #50 / Type II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #50 / Type II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Heat-labile enterotoxin IIB, A chain / Heat-labile enterotoxin IIB, B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, FIVE-FOLD AVERAGING, HOMOLOGY MODEL / Resolution: 2.25 Å
AuthorsVan Den Akker, F. / Hol, W.G.J.
Citation
Journal: Structure / Year: 1996
Title: Crystal structure of a new heat-labile enterotoxin, LT-IIb.
Authors: van den Akker, F. / Sarfaty, S. / Twiddy, E.M. / Connell, T.D. / Holmes, R.K. / 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. / Witholt, B. / Hol, W.G.
#2: Journal: J.Bacteriol. / Year: 1989
Title: Cloning, Nucleotide Sequence, and Hybridization Studies of the Type Iib Heat-Labile Enterotoxin Gene of Escherichia Coli
Authors: Pickett, C.L. / Twiddy, E.M. / Coker, C. / Holmes, R.K.
History
DepositionMar 20, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HEAT LABILE ENTEROTOXIN TYPE IIB
E: HEAT LABILE ENTEROTOXIN TYPE IIB
F: HEAT LABILE ENTEROTOXIN TYPE IIB
G: HEAT LABILE ENTEROTOXIN TYPE IIB
H: HEAT LABILE ENTEROTOXIN TYPE IIB
A: HEAT LABILE ENTEROTOXIN TYPE IIB
C: HEAT LABILE ENTEROTOXIN TYPE IIB


Theoretical massNumber of molelcules
Total (without water)81,1347
Polymers81,1347
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-128 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.700, 105.700, 171.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
HEAT LABILE ENTEROTOXIN TYPE IIB / LT-IIB


Mass: 10778.190 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: LATENT/INACTIVE FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Plasmid: BLUESCRIPT-KS VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: P43529
#2: Protein HEAT LABILE ENTEROTOXIN TYPE IIB / LT-IIB


Mass: 21334.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LATENT/INACTIVE FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Plasmid: BLUESCRIPT-KS VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: P43528
#3: Protein HEAT LABILE ENTEROTOXIN TYPE IIB / LT-IIB


Mass: 5908.632 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LATENT/INACTIVE FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Plasmid: BLUESCRIPT-KS VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: P43528
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ASYMMETRIC UNIT CONTAINS ONE AB5 TOXIN HEXAMER. THE A SUBUNIT CONTAINS TWO FRAGMENTS LINKED BY ...THE ASYMMETRIC UNIT CONTAINS ONE AB5 TOXIN HEXAMER. THE A SUBUNIT CONTAINS TWO FRAGMENTS LINKED BY A DISORDERED LOOP. THESE TWO FRAGMENTS ARE CONVENTIONALLY REFERRED TO AS A1 AND A2, WHICH ARE LABELED AS CHAINS A AND C IN THIS COORDINATE SET. FRAGMENT A1 AND A2 ARE COVALENTLY LINKED IN THE LATENT TOXIN AND ARE PROTEOLYTICALLY CLEAVED UPON ACTIVATION. THE FIVE IDENTICAL B SUBUNITS ARE LABELED AS CHAINS D, E, F, G, AND H. SUBUNIT CHAIN PROTEIN SEQUENCE A1 A 1 - 46, 48- 187 A2 C 195 - 230 B#1 D 1 - 98 B#2 E 1 - 98 B#3 F 1 - 98 B#4 G 1 - 98 B#5 H 1 - 98 WATER 1 - 215
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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: SITTING DROP VAPOR DIFFUSION RESERVOIR CONTAINS: 2.0M NACL,0.2M LI2SO4, 0.2M NA-ACETATE PH 4.7 AT 4 DEGREES CELSIUS, vapor diffusion - sitting drop, temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.0 M1reservoirNaCl
20.2 M1reservoirLi2SO4
30.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorDetector: IMAGE PLATE / Date: Mar 20, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. obs: 44164 / % possible obs: 83 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.6
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.56 / % possible all: 68

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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: SIR, FIVE-FOLD AVERAGING, HOMOLOGY MODEL
Resolution: 2.25→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.266 -5 %
Rwork0.191 --
obs0.191 43325 82.4 %
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.3633 Å20.8394 Å20 Å2
2--2.3633 Å20 Å2
3----4.7265 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5469 0 0 215 5684
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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 / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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