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- PDB-2jpy: Phylloseptin-2 -

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Basic information

Entry
Database: PDB / ID: 2jpy
TitlePhylloseptin-2
ComponentsPhylloseptin-2 protein
KeywordsANTIMICROBIAL PROTEIN / alpha helix / amphipathic character / C-Terminal Carboxyamidation
Function / homologyFrog skin active peptide family / Frog antimicrobial peptide, propeptide / Frog skin active peptide family signal and propeptide / defense response to bacterium / extracellular region / Phylloseptin-H2 / Phylloseptin-H2
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsResende, J.M. / Mendonca Moraes, C. / Almeida, F.C.L. / Prates, M.V. / Cesar, A. / Valente, A. / Bemquerer, M.P. / Pilo-Veloso, D. / Bechinger, B.
CitationJournal: Peptides / Year: 2008
Title: Solution NMR structures of the antimicrobial peptides phylloseptin-1, -2, and -3 and biological activity: The role of charges and hydrogen bonding interactions in stabilizing helix conformations
Authors: Resende, J.M. / Moraes, C.M. / Prates, M.V. / Cesar, A. / Almeida, F.C. / Mundim, N.C. / Valente, A.P. / Bemquerer, M.P. / Pilo-Veloso, D. / Bechinger, B.
History
DepositionMay 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phylloseptin-2 protein


Theoretical massNumber of molelcules
Total (without water)2,1171
Polymers2,1171
Non-polymers00
Water0
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 #1closest to the average

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Components

#1: Protein/peptide Phylloseptin-2 protein


Mass: 2117.494 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was synthesized by solid-phase synthesis using Fmoc chemistry. The peptide is an antimicrobial peptide that is naturally found from the skin secretion of Phyllomedusa ...Details: The peptide was synthesized by solid-phase synthesis using Fmoc chemistry. The peptide is an antimicrobial peptide that is naturally found from the skin secretion of Phyllomedusa hypochondrialis (Orange-legged leaf frog), a frog species found in Brazilian southeast Atlantic Forest.
References: UniProt: Q0VZ43, UniProt: P84567*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC
1412D 1H-15N HSQC

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Sample preparation

DetailsContents: 4.0 mM Phylloseptin-2, trifluoroethanol/water (60%/40%)
Solvent system: trifluoroethanol/water (60%/40%)
SampleConc.: 4.0 mM / Component: Phylloseptin-2
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
NMRView5.0.4Johnson, One Moon Scientificdata analysis
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.17.0Schwieters, Kuszewski, Tjandra and Clorerefinement
MOLMOL2k.2Koradi, Billeter and Wuthrichdata analysis
Procheck3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 194 / NOE intraresidue total count: 116 / NOE medium range total count: 32 / NOE sequential total count: 46
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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