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- PDB-6q08: Synoeca peptide was isolated from the venom of wasp synoeca surinama. -

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Basic information

Entry
Database: PDB / ID: 6q08
TitleSynoeca peptide was isolated from the venom of wasp synoeca surinama.
ComponentsSynoeca peptide
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial / peptide structure
Biological speciesSynoeca surinama (insect)
MethodSOLUTION NMR / simulated annealing
AuthorsAlves, E.S. / Rodrigues, L.V. / Liao, L.M.
CitationJournal: To Be Published
Title: NMR STRUCTURE OF THE ANTIMICROBIAL PEPTIDE ISOLATED FROM THE VENOM OF WASP Synoeca Surinama.
Authors: Alves, E.S.F. / Rodrigues, L.V. / Liao, L.M.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synoeca peptide


Theoretical massNumber of molelcules
Total (without water)1,5981
Polymers1,5981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
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 Synoeca peptide


Mass: 1598.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synoeca surinama (insect)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM synoeca, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] DSS, 90 % v/v H2O, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O
Details: A solution containing 1 mM of peptide was prepared in 300 mM of SDS-d25, 90:10 H2O/D2O and 5% of DSS, and the pH adjusted for 7.
Label: Synoeca / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMsynoecanatural abundance1
100 mMSDS-D25[U-98% 2H]1
5 % v/vDSS[U-98% 2H]1
90 % v/vH2Onatural abundance1
10 %D2O[U-99% 2H]1
Sample conditionsDetails: A solution containing 1 mM of peptide was prepared in 300 mM of SDS-d25, 90:10 H2O/D2O and 5% of DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid), and the pH adjusted for 7.
Ionic strength: neutal Not defined / Label: synoeca / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 4
Details: In the final structure calculation of synoeca-MP, 176 unique NOEs and 24 dihedral angles were used as restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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