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 34346

Title: NMR Structure of Big-defensin 1 from oyster Crassostrea gigas   PubMed: 31641083

Deposition date: 2018-12-21 Original release date: 2019-12-06

Authors: Loth, K.; Meudal, H.; Delmas, A.

Citation: Loth, K.; Vergnes, A.; Barreto, C.; Voisin, S.; Meudal, H.; Da Silva, J.; Bressan, A.; Belmadi, N.; Bachere, E.; Aucagne, V.; Cazevielle, C.; Marchandin, H.; Rosa, R.; Bulet, P.; Touqui, L.; Delmas, A.; Destoumieux-Garzon, D.. "The Ancestral N-Terminal Domain of Big Defensins Drives Bacterially Triggered Assembly into Antimicrobial Nanonets."  Mbio 10, .-. (2019).

Assembly members:
entity_1, polymer, 93 residues, 10712.988 Da.

Natural source:   Common Name: Pacific oyster   Taxonomy ID: 29159   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Crassostrea gigas

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: XAQALLPIASYAGLTVSAPV FAALVTVYGAYALYRYNIRR RENSYQRIRSDHDSHSCANN RGWCRPTCFSHEYTDWFNND VCGSYRCCRPGRX

Data sets:
Data typeCount
13C chemical shifts172
15N chemical shifts90
1H chemical shifts628

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 93 residues - 10712.988 Da.

1   PCAALAGLNALALEULEUPROILEALASER
2   TYRALAGLYLEUTHRVALSERALAPROVAL
3   PHEALAALALEUVALTHRVALTYRGLYALA
4   TYRALALEUTYRARGTYRASNILEARGARG
5   ARGGLUASNSERTYRGLNARGILEARGSER
6   ASPHISASPSERHISSERCYSALAASNASN
7   ARGGLYTRPCYSARGPROTHRCYSPHESER
8   HISGLUTYRTHRASPTRPPHEASNASNASP
9   VALCYSGLYSERTYRARGCYSCYSARGPRO
10   GLYARGAAR

Samples:

sample_1: [1-93]Cg-BigDef1 1.0 mM

sample_conditions_1: ionic strength: 0 mM; pH: 4.6; 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-13C HSQCsample_1isotropicsample_conditions_1

Software:

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

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

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AVANCE III HD 700 MHz

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