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- PDB-7d37: Solution structure of Acm2-precursor peptide of Heat-stable enter... -

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Basic information

Entry
Database: PDB / ID: 7d37
TitleSolution structure of Acm2-precursor peptide of Heat-stable enterotoxin produced by Enterotoxigenic Escherichia coli
ComponentsCYS-CY1-GLU-LEU-CYS-CYS-ASN-PRO-ALA-CY1-THR-GLY-CYS
KeywordsTOXIN / Heat-stable enterotoxin / topological isomer / STh / STh(6-18)
Function / homologyHeat-stable enterotoxin, STa / Heat-stable enterotoxin, conserved site / Heat-stable enterotoxin ST / Heat-stable enterotoxins signature. / toxin activity / extracellular space / Heat-stable enterotoxin A3/A4
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsShimamoto, S. / Hidaka, Y.
CitationJournal: Molecules / Year: 2020
Title: Topological Regulation of the Bioactive Conformation of a Disulfide-Rich Peptide, Heat-Stable Enterotoxin.
Authors: Shimamoto, S. / Fukutsuji, M. / Osumi, T. / Goto, M. / Toyoda, H. / Hidaka, Y.
History
DepositionSep 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: 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

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Assembly

Deposited unit
A: CYS-CY1-GLU-LEU-CYS-CYS-ASN-PRO-ALA-CY1-THR-GLY-CYS


Theoretical massNumber of molelcules
Total (without water)1,4621
Polymers1,4621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1290 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide CYS-CY1-GLU-LEU-CYS-CYS-ASN-PRO-ALA-CY1-THR-GLY-CYS


Mass: 1461.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P07965*PLUS
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
122isotropic12D DQF-COSY
131isotropic12D 1H-1H NOESY
142isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution12 mg/mL Acm2-precursor peptide of STh, 100% D2O50% CD3COODsample_1100% D2O
solution22 mg/mL Acm2-precursor peptide of STh, 90% H2O/10% D2O50% CD3COODsample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mg/mLAcm2-precursor peptide of SThnatural abundance1
2 mg/mLAcm2-precursor peptide of SThnatural abundance2
Sample conditionsIonic strength: 1 mM / Label: conditions_1 / pH: 3 / Pressure: 1.0 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: JEOL JNM ECA800 / Manufacturer: JEOL / Model: JNM ECA800 / Field strength: 800 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: structure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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