BMRB Entry 35024

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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/BMR35024
MolProbity Validation Chart

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Title:
NMR study of the lasso peptide syanodin I (1-16)
Deposition date:
2025-10-16
Original release date:
2026-04-22
Authors:
Santos-Fernandez, M.; Jeanne Dit Fouque, K.; Karki, U.; Blond, A.; Idir, R.; Asgharihosseinpour, N.; Zirah, S.; Chapagain, P.; Hegemann, J.; Fernandez-Lima, F.
Citation:

Citation: Santos-Fernandez, Miguel; Jeanne Dit Fouque, Kevin; Karki, Ukesh; Blond, Alain; Idir, Ryane; Asgharihosseinpour, Negin; Zirah, Severine; Chapagain, Prem; Mebel, Alexander; Hegemann, Julian; Fernandez-Lima, Francisco. "Structural Landscape of Syanodin I Lasso Peptide"  Biochemistry ., .-. (2026).
PubMed: 41979354

Assembly members:

Assembly members:
entity_1, polymer, 16 residues, 1370.467 Da.

Natural source:

Natural source:   Common Name: Sphingobium yanoikuyae   Taxonomy ID: 13690   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Sphingobium yanoikuyae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pET41a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GISGGTVDAPAGQGLA

Data sets:
Data typeCount
13C chemical shifts50
1H chemical shifts90

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 16 residues - 1370.467 Da.

1   GLYILESERGLYGLYTHRVALASPALAPRO
2   ALAGLYGLNGLYLEUALA

Samples:

sample_1: Syanodin 2 mM

sample_conditions_1: ionic strength: 0 mM; pH: 7; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HMBCsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, data analysis

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

AURELIA, Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzer - chemical shift assignment, peak picking

CHARMM, Karplus - geometry optimization

NMR spectrometers:

  • Bruker AVANCE III HD 600 MHz