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- PDB-6o3q: NMR solution structure of vicilin-buried peptide-8 (VBP-8) -

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Basic information

Entry
Database: PDB / ID: 6o3q
TitleNMR solution structure of vicilin-buried peptide-8 (VBP-8)
ComponentsVicilin
KeywordsPLANT PROTEIN / seed peptide
Function / homologyVicilin, N-terminal / Vicilin N terminal region / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Vicilin
Function and homology information
Biological speciesSolanum lycopersicum (tomato)
MethodSOLUTION NMR / simulated annealing
AuthorsRosengren, K.J. / Payne, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190102058 Australia
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: An Ancient Peptide Family Buried within Vicilin Precursors.
Authors: Zhang, J. / Payne, C.D. / Pouvreau, B. / Schaefer, H. / Fisher, M.F. / Taylor, N.L. / Berkowitz, O. / Whelan, J. / Rosengren, K.J. / Mylne, J.S.
History
DepositionFeb 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_nmr_spectrometer.model
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 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


Theoretical massNumber of molelcules
Total (without water)6,0081
Polymers6,0081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4450 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Vicilin /


Mass: 6007.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Solanum lycopersicum (tomato) / References: UniProt: B0JEU3

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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-15N HSQC
141isotropic12D 1H-13C HSQC
251isotropic12D 1H-1H NOESY
361isotropic12D 1H-1H NOESY
471isotropic12D 1H-1H NOESY
581isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 2 mg/mL VBP-8, 90% H2O/10% D2O / Label: sample_A / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mg/mL / Component: VBP-8 / Isotopic labeling: natural abundance
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
10 mMconditions_14 0.2ambient 298 K
20 mMconditions_24 0.2ambient 288 K
30 mMconditions_34 0.2ambient 293 K
40 mMconditions_44 0.2ambient 303 K
50 mMconditions_54 0.2ambient 308 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4Bruker Biospincollection
TopSpin4Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
Details: Calculated using torsion and dynamics then refined and energy minimised in explicit solvent.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 20

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