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- PDB-1lts: REFINED STRUCTURE OF E. COLI HEAT LABILE ENTEROTOXIN, A CLOSE REL... -

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Basic information

Entry
Database: PDB / ID: 1lts
TitleREFINED STRUCTURE OF E. COLI HEAT LABILE ENTEROTOXIN, A CLOSE RELATIVE OF CHOLERA TOXIN
Components
  • (HEAT-LABILE ENTEROTOXIN, SUBUNIT A) x 2
  • HEAT-LABILE ENTEROTOXIN, SUBUNIT B
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
Heat-labile enterotoxin A chain / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsSixma, T.K. / Hol, W.G.J.
Citation
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. / Van Zanten, B.A.M. / Dauter, Z. / Hol, W.G.J.
#1: 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.M. / Berghuis, A.M. / 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.
#3: Journal: Proceedings Ccp4 Study Weekend: Isomorphous Replacement and Anomalous Scattering
Year: 1991
Title: Native Non-Isomorphism in the Structure Determination of Heat Labile Enterotoxin (Lt) from E. Coli
Authors: Sixma, T.K. / Pronk, S.E. / Van Scheltinga, A.C.T. / Aguirre, A. / Kalk, K.H. / Vriend, G. / 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 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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, 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)85,3467
Polymers85,3467
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19810 Å2
ΔGint-77 kcal/mol
Surface area28210 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
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99235, -0.0652, -0.1049), (-0.0791, 0.31667, -0.9452), (0.09485, 0.94629, 0.30909)6.304, 61.103, -20.062
2given(0.97997, -0.1845, -0.075), (-0.1931, -0.7891, -0.583), (0.04853, 0.58588, -0.8089)10.676, 98.917, 32.163
3given(0.97998, -0.1931, 0.0485), (-0.1845, -0.7891, 0.5859), (-0.0748, -0.5831, -0.809)7.079, 61.183, 84.496
4given(0.9923, -0.079, 0.0949), (-0.0652, 0.31667, 0.9463), (-0.1049, -0.9452, 0.3091)0.478, 0.046, 64.619
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 INCLUDED IN MTRIX CARDS RELATE B-PENTAMERS VIA FIVEFOLD AXIS: KAPPA PHI PSI RELATING 288.0 0.4 96.0 B1 TO B2 (MTRIX1) 216.0 0.4 96.0 B1 TO B3 (MTRIX2) 144.0 0.4 96.0 B1 TO B4 (MTRIX3) 72.0 0.4 96.0 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


Mass: 11807.539 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / 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) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P06717
#3: Protein/peptide HEAT-LABILE ENTEROTOXIN, SUBUNIT A


Mass: 4953.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P06717
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS THE UNNICKED AND UNREDUCED FORM OF THE TOXIN.
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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal grow
*PLUS
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: 1.95 Å / Lowest resolution: 9999 Å / Num. obs: 53762 / % possible obs: 94.4 % / Num. measured all: 230816 / Rmerge(I) obs: 0.088

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.95→8 Å / σ(F): 0
Details: MEAN TEMPERATURE FACTORS ARE HIGH. (SEE SUBUNIT NUMBERING SCHEME, REMARK 10).
RfactorNum. reflection
obs0.182 52397
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 0 293 6271
Refinement
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 8 Å / Num. reflection all: 52397 / σ(F): 0 / Rfactor all: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.15
X-RAY DIFFRACTIONo_angle_deg3
X-RAY DIFFRACTIONo_dihedral_angle_d24.9
X-RAY DIFFRACTIONo_dihedral_angle_deg1.24

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