BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30579

Title: NMR solution structure of vicilin-buried peptide-8 (VBP-8)   PubMed: 30973714

Deposition date: 2019-02-27 Original release date: 2019-04-18

Authors: Rosengren, K.; Payne, C.

Citation: Zhang, J.; Payne, C.; Pouvreau, B.; Schaefer, H.; Fisher, M.; Taylor, N.; Berkowitz, O.; Whelan, J.; Rosengren, K.; Mylne, J.. "An ancient peptide family buried within vicilin precursors."  ACS Chem. Biol. 14, 979-993 (2019).

Assembly members:
entity_1, polymer, 49 residues, 6007.551 Da.

Natural source:   Common Name: Tomato   Taxonomy ID: 4081   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Solanum lycopersicum

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: RGPDKSYKRLQECQRRCQSE QQGQRLQECQQRCQQEYQRE KGQHQGETN

Data sets:
Data typeCount
13C chemical shifts90
15N chemical shifts46
1H chemical shifts316

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 49 residues - 6007.551 Da.

1   ARGGLYPROASPLYSSERTYRLYSARGLEU
2   GLNGLUCYSGLNARGARGCYSGLNSERGLU
3   GLNGLNGLYGLNARGLEUGLNGLUCYSGLN
4   GLNARGCYSGLNGLNGLUTYRGLNARGGLU
5   LYSGLYGLNHISGLNGLYGLUTHRASN

Samples:

sample_1: VBP-8 2 mg/mL

sample_conditions_1: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 288 K

sample_conditions_3: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 293 K

sample_conditions_4: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 303 K

sample_conditions_5: ionic strength: 0 mM; pH: 4; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_3
2D 1H-1H NOESYsample_1isotropicsample_conditions_4
2D 1H-1H NOESYsample_1isotropicsample_conditions_5

Software:

TopSpin v4, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA v3.9, Guntert, Mumenthaler and Wuthrich - structure calculation

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Bruker Avance III 700 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts