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- PDB-7l55: Solution NMR structure of the cyclic plant protein PDP-23 in DPC ... -

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Basic information

Entry
Database: PDB / ID: 7l55
TitleSolution NMR structure of the cyclic plant protein PDP-23 in DPC micelles
ComponentsCyclic plant protein PDP-23
KeywordsPLANT PROTEIN / paws derived peptide / macrocycle
Biological speciesZinnia elegans (garden zinnia)
MethodSOLUTION NMR / simulated annealing
AuthorsPayne, C.D. / Rosengren, K.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190102058 Australia
CitationJournal: Chem Sci / Year: 2021
Title: A chameleonic macrocyclic peptide with drug delivery applications.
Authors: Payne, C.D. / Franke, B. / Fisher, M.F. / Hajiaghaalipour, F. / McAleese, C.E. / Song, A. / Eliasson, C. / Zhang, J. / Jayasena, A.S. / Vadlamani, G. / Clark, R.J. / Minchin, R.F. / Mylne, J.S. / Rosengren, K.J.
History
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic plant protein PDP-23


Theoretical massNumber of molelcules
Total (without water)3,1361
Polymers3,1361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Monomeric form is fully supported by all NOESY data.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with acceptable covalent geometry, structures with lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cyclic plant protein PDP-23


Mass: 3135.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zinnia elegans (garden zinnia)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-13C HSQC
251isotropic12D 1H-1H TOCSY
461isotropic12D 1H-1H TOCSY
381isotropic12D 1H-1H TOCSY
571isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: micelle / Contents: 2 mg/mL PDP-23, 12 mM DPC, 90% H2O/10% D2O / Label: PDP-23 with DPC micelles / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mg/mLPDP-23natural abundance1
12 mMDPCnatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 mMPDP-23 with DPC micelles 298K5ambient 298 K
20 mMPDP-23 with DPC micelles 288K5ambient 288 K
40 mMPDP-23 with DPC micelles 293K5ambient 293 K
30 mMPDP-23 with DPC micelles 303K5ambient 303 K
50 mMPDP-23 with DPC micelles 308K5ambient 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz / Details: with cryoprobe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
Refinement
MethodSoftware ordinalDetails
simulated annealing5Simulated annealing using torsion angle dynamics
simulated annealing7Refinement in explicit water using Cartesian space
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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