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- PDB-2ndm: NMR solution structure of PawS Derived Peptide 21 (PDP-21) -

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Basic information

Entry
Database: PDB / ID: 2ndm
TitleNMR solution structure of PawS Derived Peptide 21 (PDP-21)
ComponentsPawS derived peptide 21
KeywordsPLANT PROTEIN / PDP / plant peptide / cyclic peptide
Function / homologyPawS derived peptide 21
Function and homology information
Biological speciesZinnia haageana (plant)
MethodSOLUTION NMR / simulated annealing
Model detailsstructure with best MOLPROBITY score, model1
AuthorsFranke, B. / Jayasena, A.S. / Fisher, M.F. / Swedberg, J.E. / Taylor, N.L. / Mylne, J.S. / Rosengren, K.
CitationJournal: Biopolymers / Year: 2016
Title: Diverse cyclic seed peptides in the Mexican zinnia (Zinnia haageana).
Authors: Franke, B. / Jayasena, A.S. / Fisher, M.F. / Swedberg, J.E. / Taylor, N.L. / Mylne, J.S. / Rosengren, K.J.
History
DepositionJul 17, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PawS derived peptide 21


Theoretical massNumber of molelcules
Total (without water)1,4881
Polymers1,4881
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)20 / 50structures with best MOLPROBITY score
RepresentativeModel #1structure with best molprobity score

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Components

#1: Protein/peptide PawS derived peptide 21


Mass: 1487.680 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Assembled by Fmoc solid phase peptide synthesis and cyclised by native chemical ligation.
Source: (synth.) Zinnia haageana (plant) / References: UniProt: A0A1C7D043*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
1322D 1H-13C HSQC
1412D 1H-15N HSQC
1512D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mg/mL PawS Derived Peptide 21 (PDP-21), 90% H2O/10% D2O90% H2O/10% D2O
22 mg/mL PawS Derived Peptide 21 (PDP-21), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mg/mLPawS Derived Peptide 21 (PDP-21)-11
2 mg/mLPawS Derived Peptide 21 (PDP-21)-22
Sample conditionspH: 5.2 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
ccpNmrccpnmrdata analysis
ccpNmrccpnmrpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Torsion angle dynamics
NMR representativeSelection criteria: structure with best molprobity score
NMR ensembleConformer selection criteria: structures with best MOLPROBITY score
Conformers calculated total number: 50 / Conformers submitted total number: 20

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