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 30720

Title: Solution structure of antifungal plant defensin PvD1   PubMed: 32787086

Deposition date: 2020-02-03 Original release date: 2020-08-21

Authors: Harvey, P.

Citation: Skalska, Julia; Andrade, Vitor; Cena, Gabrielle; Harvey, Peta; Gaspar, Diana Maria Diez; Mello, Erica; Troeira Henriques, Sonia; Valle, Javier; Gomes, Valdirene; Conceicao, Katia; Castanho, Miguel; Andreu, David. "Synthesis, structure, and activity of the antifungal plant defensin PvD1"  J. Med. Chem. ., .-. (2020).

Assembly members:
Knot1 domain-containing protein, polymer, 47 residues, 5459.170 Da.

Natural source:   Common Name: Kidney bean   Taxonomy ID: 3885   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Phaseolus vulgaris

Experimental source:   Production method: .

Entity Sequences (FASTA):
Knot1 domain-containing protein: KTCENLADTYKGPCFTTGSC DDHCKNKEHLRSGRCRDDFR CWCTKNC

Data sets:
Data typeCount
13C chemical shifts118
15N chemical shifts25
1H chemical shifts293

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 47 residues - 5459.170 Da.

1   LYSTHRCYSGLUASNLEUALAASPTHRTYR
2   LYSGLYPROCYSPHETHRTHRGLYSERCYS
3   ASPASPHISCYSLYSASNLYSGLUHISLEU
4   ARGSERGLYARGCYSARGASPASPPHEARG
5   CYSTRPCYSTHRLYSASNCYS

Samples:

sample_1: PvD1 1.0 mM

sample_2: PvD1 1.0 mM

sample_conditions_1: pH: 3.5; pressure: 1 atm; temperature: 298 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-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-1H ECOSYsample_2isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - processing

CcpNmr Analysis, CCPN - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Bruker AVANCE III 600 MHz

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