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 21033

Title: Solution structure of Lewis x (Gal-beta1,4-[Fuc-alpha1,3]-GlcNAc-beta) attached to a protein   PubMed: 24001318

Authors: Zierke, Mirko; Ernst, Beat; Allain, Frederic; Schubert, Mario

Citation: Zierke, Mirko; Smiesko, Martin; Rabbani, Said; Aeschbacher, Thomas; Cutting, Brian; Allain, Frederic; Schubert, Mario; Ernst, Beat. "Stabilization of Branched Oligosaccharides: Lewis(x) Benefits from a Nonconventional C-H...O Hydrogen Bond"  J. Am. Chem. Soc. 135, 13464-13472 (2013).

Assembly members:
SUGAR_(3-MER), polymer, 4 residues, 543.521 Da.
FimH, polymer, 173 residues, Formula weight is not available

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
SUGAR_(3-MER): XXXX
FimH: FACKTANGTAIPIGGGSANV YVNLAPVVNVGQNLVVDLST QIFCHNDYPETITDYVTLQR GSAYGGVLSNFSGTVKYCGS SYPFPTTSETPRVVYNSRTD KPWPVALYLTPVSSAGGVAI KAGSLIAVLILRQTNNYNSD DFQFVWNIYANNDVVVPTGL VPRGSLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts20
1H chemical shifts28

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Lewisx1
2Protein FimH2

Entities:

Entity 1, Lewisx 4 residues - 543.521 Da.

1   SP8aNAGGALFUC

Entity 2, Protein FimH 173 residues - Formula weight is not available

1   PHEALACYSLYSTHRALAASNGLYTHRALA
2   ILEPROILEGLYGLYGLYSERALAASNVAL
3   TYRVALASNLEUALAPROVALVALASNVAL
4   GLYGLNASNLEUVALVALASPLEUSERTHR
5   GLNILEPHECYSHISASNASPTYRPROGLU
6   THRILETHRASPTYRVALTHRLEUGLNARG
7   GLYSERALATYRGLYGLYVALLEUSERASN
8   PHESERGLYTHRVALLYSTYRCYSGLYSER
9   SERTYRPROPHEPROTHRTHRSERGLUTHR
10   PROARGVALVALTYRASNSERARGTHRASP
11   LYSPROTRPPROVALALALEUTYRLEUTHR
12   PROVALSERSERALAGLYGLYVALALAILE
13   LYSALAGLYSERLEUILEALAVALLEUILE
14   LEUARGGLNTHRASNASNTYRASNSERASP
15   ASPPHEGLNPHEVALTRPASNILETYRALA
16   ASNASNASPVALVALVALPROTHRGLYLEU
17   VALPROARGGLYSERLEUGLUHISHISHIS
18   HISHISHIS

Samples:

sample_1: SUGAR (3-MER) 0.5 mM; FimH 0.5 mM; D2O 100%

sample_2: SUGAR (3-MER) 0.5 mM; FimH 0.5 mM; H2O 93%; D2O 7%

sample_conditions_1: pH: 7.0; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D F1 13C-filtered 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HMQC-COSYsample_1isotropicsample_conditions_1
2D F1/F2 13C-filtered 1H-1H NOESYsample_1isotropicsample_conditions_1
2D F1/F2 15N-filtered 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, processing

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 900 MHz

Related Database Links:

BMRB 19066 19254 19255 19256 26541
PDB
DBJ BAB38702 BAE78313 BAG80117 BAI28639 BAI33780
EMBL CAA12423 CAA29156 CAH55784 CAM92099 CAP78801
GB AAA97216 AAB29812 AAC35864 AAC77276 AAD44319
REF NP_313306 NP_418740 NP_709914 WP_000816510 WP_000816511
SP P08191