BMRB Entry 30854

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30854
MolProbity Validation Chart

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Title:
NMR solution structure of PsDef2 defensin from P. sylvestris
Deposition date:
2021-02-08
Original release date:
2022-03-25
Authors:
Nesmelova, I.; Kovaleva, V.; Hrunyk, N.; Yusypovych, Y.; Shalovylo, Y.
Citation:

Citation: Nesmelova, I.; Kovaleva, V.; Hrunyk, N.; Bukhteeva, I.; Yusypovych, Y.; Shalovylo, Y.. "Structure, dynamics, and function of PsDef2 defensin from Pinus sylvestris"  Structure 30, 753-762 (2022).
PubMed: 35334207

Assembly members:

Assembly members:
entity_1, polymer, 50 residues, 5645.629 Da.

Natural source:

Natural source:   Common Name: Scots pine   Taxonomy ID: 3349   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Pinus sylvestris

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: RMCKTPSAKFKGYCVSSTNC KNVCRTEGFPTGSCDFHITS RKCYCYKPCP

Data sets:
Data typeCount
13C chemical shifts200
15N chemical shifts51
1H chemical shifts324

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 50 residues - 5645.629 Da.

1   ARGMETCYSLYSTHRPROSERALALYSPHE
2   LYSGLYTYRCYSVALSERSERTHRASNCYS
3   LYSASNVALCYSARGTHRGLUGLYPHEPRO
4   THRGLYSERCYSASPPHEHISILETHRSER
5   ARGLYSCYSTYRCYSTYRLYSPROCYSPRO

Samples:

sample_1: defensin-2, PsDef2, [U-13C; U-15N], 0.5 mM

sample_conditions_1: ionic strength: 20 mM; pH: 4.5; 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
3D HCACOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1

Software:

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Bruker AVANCE III 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks