BMRB Entry 21054

Name: Solution structure of the amphibian egg glycan Bv9 from Bombina variegata
Published: 2017-08-30

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR21054

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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 the amphibian egg glycan Bv9 from Bombina variegata

Deposition date:

2014-01-24

Original release date:

2017-08-30

Authors:

Schubert, Mario; Allain, Frederic

Citation:

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).
PubMed: 28654715

Assembly members:

Assembly members:
SUGAR_(3-MER), polymer, 4 residues, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: 191472 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Bombina variegata

Experimental source:

Experimental source: Production method: obtained from a collaborator

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	28
1H chemical shifts	38

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Bv9	1

Entities:

Entity 1, Bv9 4 residues - Formula weight is not available

1

SP

MAG

NAG

FUC

Samples:

sample_1: SUGAR (3-MER) 1 mM; D2O 100%

sample_2: SUGAR (3-MER) 1 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 7; temperature: 273 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 TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure solution

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

NMR spectrometers:

Bruker Avance 900 MHz