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- PDB-2lde: Solution structure of the long sarafotoxin srtx-i3 -

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Basic information

Entry
Database: PDB / ID: 2lde
TitleSolution structure of the long sarafotoxin srtx-i3
ComponentsSarafotoxin-i3
KeywordsTOXIN / endothelin-like peptide
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsCordier, F. / Zorba, A. / Hajj, M. / Ducancel, F. / Servent, D. / Delepierre, M.
CitationJournal: Biochimie / Year: 2012
Title: Pharmacological and structural characterization of long-sarafotoxins, a new family of endothelin-like peptides: Role of the C-terminus extension.
Authors: Mourier, G. / Hajj, M. / Cordier, F. / Zorba, A. / Gao, X. / Coskun, T. / Herbet, A. / Marcon, E. / Beau, F. / Delepierre, M. / Ducancel, F. / Servent, D.
History
DepositionMay 24, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3Nov 6, 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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Sarafotoxin-i3


Theoretical massNumber of molelcules
Total (without water)2,9671
Polymers2,9671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Sarafotoxin-i3


Mass: 2967.405 Da / Num. of mol.: 1 / Source method: obtained synthetically
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
2412D 1H-1H TOCSY
2512D 1H-1H NOESY

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Sample preparation

DetailsContents: 3 mM srtx-i3, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 3 mM / Component: srtx-i3-1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
104.5ambient 298 K
204.5ambient 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Of the 200 calculated conformers, the 80 conformers with the lowest total energy were refined in water. The 10 refined conformers of lowest energy represent the final ensemble.
NMR constraintsNOE constraints total: 445 / NOE intraresidue total count: 183 / NOE long range total count: 20 / NOE medium range total count: 101 / NOE sequential total count: 141 / Hydrogen bond constraints total count: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.456 Å
NMR ensemble rmsDistance rms dev: 0.032 Å / Distance rms dev error: 0.005 Å

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