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- PDB-1etn: MOLECULAR STRUCTURE OF THE TOXIC DOMAIN OF HEAT-STABLE ENTEROTOXI... -

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Entry
Database: PDB / ID: 1etn
TitleMOLECULAR STRUCTURE OF THE TOXIC DOMAIN OF HEAT-STABLE ENTEROTOXIN PRODUCED BY A PATHOGENIC STRAIN OF ESCHERICHIA COLI
Components5-BETA-MERCAPTOPROPIONATE HEAT-STABLE ENTEROTOXIN
KeywordsENTEROTOXIN
Function / homologyHeat-stable enterotoxin, STa / Heat-stable enterotoxin, conserved site / Heat-stable enterotoxin ST / Heat-stable enterotoxins signature. / Intestinal infectious diseases / toxin activity / extracellular space / Heat-stable enterotoxin ST-IA/ST-P
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 0.89 Å
AuthorsSato, T. / Shimonishi, Y.
Citation
Journal: J.Biol.Chem. / Year: 1991
Title: Molecular structure of the toxin domain of heat-stable enterotoxin produced by a pathogenic strain of Escherichia coli. A putative binding site for a binding protein on rat intestinal epithelial cell membranes.
Authors: Ozaki, H. / Sato, T. / Kubota, H. / Hata, Y. / Katsube, Y. / Shimonishi, Y.
#1: Journal: Biochemistry / Year: 1994
Title: Structural Characteristics for Biological Activity of Heat-Stable Enterotoxin Produced by Enterotoxigenic Escherichia Coli: X-Ray Crystallography of Weakly Toxic and Nontoxic Analogs
Authors: Sato, T. / Ozaki, H. / Hata, Y. / Kitagawa, Y. / Katsube, Y. / Shimonishi, Y.
#2: Journal: Bull.Chem.Soc.Jpn. / Year: 1992
Title: Semi-Preparative Purification and Crystallization of Synthetic Analogs of Heat-Stable Enterotoxin of Enterotoxigenic Escherichia Coli
Authors: Sato, T. / Ito, H. / Takeda, Y. / Shimonishi, Y.
#3: Journal: Bull.Chem.Soc.Jpn. / Year: 1990
Title: Structure-Activity Relationship of Escherichia Coli Heat-Stable Enterotoxin: Role of Ala Residue at Position 14 in Toxin-Receptor Interaction
Authors: Yamasaki, S. / Sato, T. / Hidaka, Y. / Ozaki, H. / Ito, H. / Hirayama, T. / Takeda, Y. / Sugimura, T. / Tai, A. / Shimonishi, Y.
#4: Journal: FEBS Lett. / Year: 1985
Title: Essential Structure for Full Enterotoxigenic Activity of Heat-Stable Enterotoxin Produced by Enterotoxigenic Escherichia Coli
Authors: Yoshimura, S. / Ikemura, H. / Watanabe, H. / Aimoto, H. / Shimonishi, Y. / Hara, S. / Takeda, T. / Miwatani, T. / Takeda, Y.
History
DepositionMar 15, 1994Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 19, 2013Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-BETA-MERCAPTOPROPIONATE HEAT-STABLE ENTEROTOXIN


Theoretical massNumber of molelcules
Total (without water)1,2591
Polymers1,2591
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.010, 27.621, 12.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide 5-BETA-MERCAPTOPROPIONATE HEAT-STABLE ENTEROTOXIN / (MPR==5==)STP(5-17)


Mass: 1258.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 18D / References: UniProt: P01559
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IS BASED ON SEQUENCE FROM ENTEROTOXIGENIC (ESCHERICHIA COLI STRAIN 18D). THE THIRTEEN ...THE SEQUENCE IS BASED ON SEQUENCE FROM ENTEROTOXIGENIC (ESCHERICHIA COLI STRAIN 18D). THE THIRTEEN RESIDUE PEPTIDE CORRESPONDS TO RESIDUES FROM 5 TO 17.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.47 Å3/Da / Density % sol: 16.52 %
Crystal grow
*PLUS
Temperature: 24 ℃ / Method: unknown
Components of the solutions
*PLUS
Conc.: 2.5 mg/ml / Common name: enzyme

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 0.89 Å / Num. obs: 6246 / Rmerge(I) obs: 0.024

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Processing

SoftwareName: FMLS/VP / Classification: refinement
RefinementResolution: 0.89→10.9 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.088 --
obs-6246 71.4 %
Refinement stepCycle: LAST / Resolution: 0.89→10.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms82 0 0 13 95
Refinement
*PLUS
Rfactor obs: 0.088
Solvent computation
*PLUS
Displacement parameters
*PLUS

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