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- PDB-6axi: PawL-Derived Peptide PLP-2 -

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Basic information

Entry
Database: PDB / ID: 6axi
TitlePawL-Derived Peptide PLP-2
ComponentsASP-LEU-PHE-VAL-PRO-PRO-ILE-ASP
KeywordsDE NOVO PROTEIN / orbitide / cyclic peptide / plant peptide / buried peptide
Biological speciesSenecio pinnatifolius (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsFisher, M. / Mylne, J.S. / Howard, M.J.
CitationJournal: Plant Direct / Year: 2018
Title: A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch.
Authors: Fisher, M.F. / Zhang, J. / Taylor, N.L. / Howard, M.J. / Berkowitz, O. / Debowski, A.W. / Behsaz, B. / Whelan, J. / Pevzner, P.A. / Mylne, J.S.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASP-LEU-PHE-VAL-PRO-PRO-ILE-ASP


Theoretical massNumber of molelcules
Total (without water)9151
Polymers9151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1030 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide ASP-LEU-PHE-VAL-PRO-PRO-ILE-ASP


Mass: 915.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Senecio pinnatifolius (plant)

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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-1H COSY
141isotropic12D 1H-13C HMBC
151isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 2.0 mg/mL NA PLP-2, 90% H2O/10% D2O / Label: PLP-2 / Solvent system: DMSO
SampleConc.: 2.0 mg/mL / Component: PLP-2 / Isotopic labeling: NA
Sample conditionsIonic strength: 2.4 mM / Ionic strength err: 0.2 / Label: 298 K / pH: 4.5 / PH err: 0.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
CcpNMR2.4.2CCPNdata analysis
YASARA16.7.22Elmar Kriegerrefinement
YASARA16.7.22Elmar Kriegerstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
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: 20

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