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 21032

Title: Solution structure of 1,3-Fucosylated chitobiose   PubMed: 28654715

Authors: Schubert, Mario; Allain, Frederic; Aeschbacher, Thomas

Citation: Aeschbacher, Thomas; Zierke, Mirko; Smiesko, Martin; Collot, Mayeul; Mallet, Jean-Maurice; Ernst, Beat; Allain, Frederic H-T; Schubert, Mario. "A Secondary Structural Element in a Wide Range of Fucosylated Glycoepitopes."  Chemistry 23, 11598-11610 (2017).

Assembly members:
SUGAR_(3-MER), polymer, 4 residues, 684.69 Da.

Natural source:   Common Name: nematode   Taxonomy ID: 6239   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Caenorhabditis elegans

Experimental source:   Production method: chemically synthesized

Entity Sequences (FASTA):
SUGAR_(3-MER): XXXX

Data sets:
Data typeCount
13C chemical shifts52
1H chemical shifts78

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1SUGAR (3-MER)1

Entities:

Entity 1, SUGAR (3-MER) 4 residues - 684.69 Da.

The trisaccharide contains twice NAG, the terminal NAG (residue 3) is linked to O4 of the proximal NAG. The Proximal NAG (residue 2) is linked via O3 to FUC (residue 4) and via C1 to O6 of 6HH (residue 1).

1   6HHNAGNAGFUC

Samples:

sample_1: SUGAR (3-MER) 2.8 mM; D2O 100%

sample_2: SUGAR (3-MER) 2.8 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 7; temperature: 277 K

sample_conditions_2: pH: 7; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_2
2D 1H-1H TOCSYsample_1isotropicsample_conditions_2
2D 1H-13C HSQC long rangesample_1isotropicsample_conditions_2

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 900 MHz

Related Database Links: