BMRB Entry 19748

Name: Solution structure of Lactodifucotetraose (LDFT) beta anomer
Published: 2016-06-29

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PDB ID: 2mk1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19748
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of Lactodifucotetraose (LDFT) beta anomer

Deposition date:

2014-01-22

Original release date:

2016-06-29

Authors:

Schubert, Mario; Allain, Frederic

Citation:

Citation: Aeschbacher, Thomas; Zierke, Mirko; Smiesko, Martin; Allain, Frederic; Schubert, Mario. "Fucosylated glycans" .

Assembly members:

Assembly members:
SUGAR_(4-MER), polymer, 4 residues, 634.584 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: Carbosynth (vendor)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SUGAR_(4-MER): XXXX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	24
1H chemical shifts	30

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SUGAR (4-MER)	1

Entities:

Entity 1, SUGAR (4-MER) 4 residues - 634.584 Da.

The polymer type "GLYCAN" would fit much better. This entry consists of D and L sugars. the molecule is: FUC-alpha1,2-GAL-beta1,4-[FUC-alpha1,3]-BGC-beta-OH The BGC is covalently linked to Fuc and Gal. The GAL is covalently linked to Fuc and BGC. The two Fuc units are covalently linked either to BGC or GAL.

1

BGC

GAL

FUC

Samples:

sample_1: SUGAR (4-MER) 3.2 mM

sample_conditions_1: ionic strength: 0 M; pH: 7; pressure: 1 atm; temperature: 275 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

SPARKY, Goddard - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker Avance 900 MHz