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- PDB-7m3u: Solution NMR Structure of PawS-Derived Peptide PDP-24 -

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Basic information

Entry
Database: PDB / ID: 7m3u
TitleSolution NMR Structure of PawS-Derived Peptide PDP-24
ComponentsPawS-Derived Peptide PDP-24
KeywordsPLANT PROTEIN / Cyclic / AEP-processed / bi-disulfide
Biological speciesZinnia haageana (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsPayne, C.D. / Rosengren, K.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190102058 Australia
CitationJournal: Rsc Chem Biol / Year: 2021
Title: Solution NMR and racemic crystallography provide insights into a novel structural class of cyclic plant peptides.
Authors: Payne, C.D. / Vadlamani, G. / Hajiaghaalipour, F. / Muhammad, T. / Fisher, M.F. / Andersson, H.S. / Goransson, U. / Clark, R.J. / Bond, C.S. / Mylne, J.S. / Rosengren, K.J.
History
DepositionMar 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PawS-Derived Peptide PDP-24


Theoretical massNumber of molelcules
Total (without water)3,0381
Polymers3,0381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: monomeric structure is fully consistent with NOESY data
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PawS-Derived Peptide PDP-24


Mass: 3038.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zinnia haageana (plant)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
311isotropic12D 1H-1H TOCSY
321isotropic12D 1H-1H NOESY
332isotropic12D 1H-13C HSQC
341isotropic12D 1H-15N HSQC
151isotropic12D 1H-1H TOCSY
281isotropic12D 1H-1H TOCSY
471isotropic12D 1H-1H TOCSY
561isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mg/mL PDP-24, 80% CD3CN/20% H2OPDP-2480% CD3CN/20% H2O
solution22 mg/mL PDP-24, 80% CD3CN/20% D2OPDP-24 D2O80% CD3CN/20% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mg/mLPDP-24natural abundance1
2 mg/mLPDP-24natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 mM288K3.51 atm288 K
20 mM293K3.51 atm293 K
30 mM298K3.51 atm298 K
40 mM303K3.51 atm303 K
50 mM308K3.51 atm308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Refinement
MethodSoftware ordinalDetails
simulated annealing5using torsion angle dynamics
simulated annealing2using torsion angle dynamics and Cartesian space
simulated annealing1structures minimized in explicit water using Cartesian dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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