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- PDB-7l51: Solution NMR structure of the dimeric form of the cyclic plant pr... -

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Basic information

Entry
Database: PDB / ID: 7l51
TitleSolution NMR structure of the dimeric form of the cyclic plant protein PDP-23 in H2O
ComponentsCyclic plant protein PDP-23
KeywordsPLANT PROTEIN / macrocyclic peptide / paws derived peptide
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
B: Cyclic plant protein PDP-23


Theoretical massNumber of molelcules
Total (without water)6,2712
Polymers6,2712
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Assembly evident from large number of intermolecular NOEs
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1480 Å2
ΔGint-15 kcal/mol
Surface area3710 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with acceptable covalent geometry, structures with the 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.: 2 / 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
111isotropic21D
121isotropic22D 1H-1H TOCSY
131isotropic22D 1H-1H NOESY
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC
571isotropic12D 1H-1H TOCSY
481isotropic12D 1H-1H TOCSY
391isotropic12D 1H-1H TOCSY
261isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 2 mg/mL PDP-23, 90% H2O/10% D2O / Details: PDP-23 (~1mg) dissolved in 550 ul 90:10 H2O/D2O / Label: PDP-23 / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mg/mL / Component: PDP-23 / Isotopic labeling: natural abundance
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1298 K for structure determination0 mMPDP-23 298K5 ambient 298 K
5288 K for HN Temperature Coefficient data0 mMPDP-23 288K5 ambient 288 K
4293 K for HN Temperature Coefficient data0 mMPDP-23 293K5 ambient 293 K
3303 K for HN Temperature Coefficient data0 mMPDP-23 303K5 ambient 303 K
2308 K for HN Temperature Coefficient data0 mMPDP-23 308K5 ambient 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD7001with cryoprobe
Bruker AVANCE III HDBrukerAVANCE III HD6002with cryoprobe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
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 annealing4Simulated 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 the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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