BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 25468

Title: Solution NMR Structure of PDFL2.1 from Arabidopsis thaliana   PubMed: 27592418

Deposition date: 2015-02-05 Original release date: 2016-02-15

Authors: Omidvar, Reza; Bohlmann, Holger; Xia, Youlin; Veglia, Gianluigi

Citation: Omidvar, Reza; Xia, Youlin; Porcelli, Fernando; Bohlmann, Holger; Veglia, Gianluigi. "NMR structure and conformational dynamics of AtPDFL2.1, a defensin-like peptide from Arabidopsis thaliana."  Biochim. Biophys. Acta 1864, 1739-1747 (2016).

Assembly members:
entity, polymer, 55 residues, 6152.270 Da.

Natural source:   Common Name: thale cress   Taxonomy ID: 3702   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Arabidopsis thaliana

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity: KDIDGRKPLLIGTCIEFPTE KCNKTCIESNFAGGKCVHIG QSLDFVCVCFPKYYI

Data sets:
Data typeCount
13C chemical shifts161
15N chemical shifts55
1H chemical shifts386

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 55 residues - 6152.270 Da.

1   LYSASPILEASPGLYARGLYSPROLEULEU
2   ILEGLYTHRCYSILEGLUPHEPROTHRGLU
3   LYSCYSASNLYSTHRCYSILEGLUSERASN
4   PHEALAGLYGLYLYSCYSVALHISILEGLY
5   GLNSERLEUASPPHEVALCYSVALCYSPHE
6   PROLYSTYRTYRILE

Samples:

sample_1: entity, [U-13C; U-15N], 1 mM; potassium chloride 40 mM; potassium phosphate 20 mM; sodium azide 1 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.16 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1

Software:

X-PLOR_NIH v2.37, Charles Schwieters - structure solution

NMRPipe v7.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.113, Goddard - chemical shift assignment, peak picking

TALOS v3.80F1, Cornilescu, Delaglio and Bax - geometry optimization

TOPSPIN v3.1, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 850 MHz
  • Bruker Avance 700 MHz

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