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- PDB-6wql: Solution structure of the seed peptide C2 (VBP-1) from pumpkin -

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Basic information

Entry
Database: PDB / ID: 6wql
TitleSolution structure of the seed peptide C2 (VBP-1) from pumpkin
ComponentsSeed peptide C2 (VBP-1)
KeywordsPLANT PROTEIN / vicilin-buried peptide
Function / homologyCupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / PV100
Function and homology information
Biological speciesCucurbita maxima (winter squash)
MethodSOLUTION NMR / simulated annealing
AuthorsPayne, C.P. / Rosengren, K.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190102058 Australia
CitationJournal: J.Nat.Prod. / Year: 2020
Title: Defining the Familial Fold of the Vicilin-Buried Peptide Family.
Authors: Payne, C.D. / Vadlamani, G. / Fisher, M.F. / Zhang, J. / Clark, R.J. / Mylne, J.S. / Rosengren, K.J.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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: Seed peptide C2 (VBP-1)


Theoretical massNumber of molelcules
Total (without water)5,8441
Polymers5,8441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NOEs are fully consistent with a monomer.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Seed peptide C2 (VBP-1)


Mass: 5844.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cucurbita maxima (winter squash) / References: UniProt: Q9ZWI3
Has ligand of interestN

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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-13C HSQC
141isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 2 mg/mL C2, 90% H2O/10% D2O / Label: C2_(VBP-1)_H2O-D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mg/mL / Component: C2 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: C2 / pH: 3.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
Details: Cyana for initial calculations for Inter-proton distance restraints, CNS for refinement in explicit water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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