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- PDB-1etm: STRUCTURAL CHARACTERISTICS FOR BIOLOGICAL ACTIVITY OF HEAT-STABLE... -

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Entry
Database: PDB / ID: 1etm
TitleSTRUCTURAL CHARACTERISTICS FOR BIOLOGICAL ACTIVITY OF HEAT-STABLE ENTEROTOXIN PRODUCED BY ENTEROTOXIGENIC ESCHERICHIA COLI: X-RAY CRYSTALLOGRAPHY OF WEAKLY TOXIC AND NONTOXIC ANALOGS
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: 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.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Molecular Structure of the Toxic Domain of Heat-Stable Enterotoxin Produced by a Pathogenic Strain of Escherichia Coli
Authors: Ozaki, H. / Sato, T. / Kubota, H. / Hata, Y. / Katsube, 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, S. / 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 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)1,3011
Polymers1,3011
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.862, 33.032, 12.451
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== / LEU==13==)STP(5-17)


Mass: 1300.635 Da / Num. of mol.: 1 / Mutation: A13L
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.: 10 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN SITE RECORDS BELOW, LEU 13 IS ALA 13 IN NATURAL TOXIN.
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, ALA 13 REPLACED BY LEU.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.41 Å3/Da

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 0.89 Å / Num. obs: 6046 / Num. measured all: 12749 / Rmerge(I) obs: 0.025

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Processing

SoftwareName: FMLS/VP / Classification: refinement
RefinementResolution: 0.89→16.5 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.065 --
obs-6046 84.7 %
Refinement stepCycle: LAST / Resolution: 0.89→16.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms85 0 0 10 95
Refinement
*PLUS
Rfactor obs: 0.065
Solvent computation
*PLUS
Displacement parameters
*PLUS

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