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- PDB-6wqj: Solution structure of vicilin-buried peptide-10 from cucumber -

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Basic information

Entry
Database: PDB / ID: 6wqj
TitleSolution structure of vicilin-buried peptide-10 from cucumber
ComponentsVicilin-buried peptide-10
KeywordsPLANT PROTEIN
Function / homologyCupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Uncharacterized protein
Function and homology information
Biological speciesCucumis sativus (cucumber)
MethodSOLUTION NMR / simulated annealing
AuthorsPayne, C.D. / 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: Vicilin-buried peptide-10


Theoretical massNumber of molelcules
Total (without water)4,3291
Polymers4,3291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: All NOEs consistent with a monomer structure.
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 Vicilin-buried peptide-10


Mass: 4328.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cucumis sativus (cucumber) / References: UniProt: A0A0A0L4Q9
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 TOCSY
121isotropic12D NOESY
131isotropic12D 1H-13C HSQC
242isotropic12D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.5 mg/mL VBP-10, 90% H2O/10% D2OVBP-10_H2O-D2O90% H2O/10% D2O
solution21.5 mg/mL VBP-10, 100% D2OVBP-10_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mg/mLVBP-10natural abundance1
1.5 mg/mLVBP-10natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
10 mMVBP-10_H2O-D2O3.5 0.21 atm298 K
20 mMVBP-10_D2O3.5 0.31 atm298 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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