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 30561

Title: NMR solution structure of Pisum sativum defensin 2 (Psd2) provides evidence for the presence of hydrophobic surface clusters   PubMed: 31294889

Deposition date: 2019-01-16 Original release date: 2019-08-16

Authors: Pinheiro-Aguiar, R.; Amaral, V.; Bastos, I.; Kurtenbach, E.; Almeida, F.

Citation: Pinheiro-Aguiar, R.; do Amaral, V.; Pereira, I.; Kurtenbach, E.; Almeida, F.. "Nuclear magnetic resonance solution structure of Pisum sativum defensin 2 provides evidence for the presence of hydrophobic surface-clusters."  Proteins ., .-. (2019).

Assembly members:
entity_1, polymer, 47 residues, 5414.161 Da.

Natural source:   Common Name: Garden pea   Taxonomy ID: 3888   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Pisum sativum

Experimental source:   Production method: recombinant technology   Host organism: Komagataella pastoris

Entity Sequences (FASTA):
entity_1: KTCENLSGTFKGPCIPDGNC NKHCRNNEHLLSGRCRDDFR CWCTNRC

Data sets:
Data typeCount
13C chemical shifts171
15N chemical shifts44
1H chemical shifts274

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 47 residues - 5414.161 Da.

1   LYSTHRCYSGLUASNLEUSERGLYTHRPHE
2   LYSGLYPROCYSILEPROASPGLYASNCYS
3   ASNLYSHISCYSARGASNASNGLUHISLEU
4   LEUSERGLYARGCYSARGASPASPPHEARG
5   CYSTRPCYSTHRASNARGCYS

Samples:

sample_1: Psd2, [U-13C; U-15N], 1 ± 0.005 mM; phosphate buffer 20 mM; NaCl 10 mM

sample_2: Psd2 1 ± 0.005 mM; phosphate buffer 20 mM; NaCl 10 mM

sample_conditions_1: ionic strength: 0.012 M; pH: 5.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1anisotropicsample_conditions_1
2D 1H-13C HSQCsample_1anisotropicsample_conditions_1
3D HNCACBsample_1anisotropicsample_conditions_1
3D CBCA(CO)NHsample_1anisotropicsample_conditions_1
3D HNCAsample_1anisotropicsample_conditions_1
3D HN(CO)CAsample_1anisotropicsample_conditions_1
3D HNCOsample_1anisotropicsample_conditions_1
3D HBHA(CO)NHsample_1anisotropicsample_conditions_1
3D HCCH-TOCSYsample_1anisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1anisotropicsample_conditions_1
2D 1H-1H NOESYsample_1anisotropicsample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

TopSpin, Bruker Biospin - collection

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