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 28050

Title: 1H 15N 13C Resonance Assignments of Receptor Binding Domain 1 of CDTb   PubMed: 31896582

Deposition date: 2019-11-27 Original release date: 2019-12-04

Authors: Cook, Mary; Varney, Kristen; Godoy-Ruiz, Raquel; Weber, David

Citation: Weber, David; Xu, Xingjian; Godoy-Ruiz, Raquel; Adipietro, Kaylin A. Adipietro; Peralta, Christopher; Ben-Hail, Danya; Varney, Kristen; Cook, Mary; Roth, Braden; Wilder, Paul; Cleveland, Thomas; Grishaev, Alexander; Neu, Heather M. Neu; Michel, Sarah; Yu, Wenbo; Beckett, Dorothy; Rustandi, Richard; Lancaster, Catherine; Loughney, John; Kristopeit, Adam; Christanti, Sianny; Olson, Jessica; MacKerell, Alex; des Georges, Amedee; Pozharski, Edwin. "Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a novel macromolecular assembly"  Proc. Natl. Acad. Sci. U.S.A. 117, 1049-1058 (2020).

Assembly members:
CDTb_receptor_binding_domain_1, polymer, 136 residues, Formula weight is not available
entity_CA, non-polymer, 40.078 Da.

Natural source:   Common Name: Clostridium difficile   Taxonomy ID: 1496   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Clostridium difficile

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
CDTb_receptor_binding_domain_1: DDDDKPTYFTNFDDYNNYPS TWSNVNTTNQDGLQGSANKL NGETKIKIPMSELKPYKRYV FSGYSKDPLTSNSIIVKIKA KEEKTDYLVPEQGYTKFSYE FETTEKDSSNIEITLIGSGT TYLDNLSITELNSTPE

Data sets:
Data typeCount
13C chemical shifts437
15N chemical shifts119
1H chemical shifts119

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RBD1, chain 11
2RBD1, chain 21
3RBD1, chain 31
4RBD1, chain 41
5CALCIUM ION2

Entities:

Entity 1, RBD1, chain 1 136 residues - Formula weight is not available

1   ASPASPASPASPLYSPROTHRTYRPHETHR
2   ASNPHEASPASPTYRASNASNTYRPROSER
3   THRTRPSERASNVALASNTHRTHRASNGLN
4   ASPGLYLEUGLNGLYSERALAASNLYSLEU
5   ASNGLYGLUTHRLYSILELYSILEPROMET
6   SERGLULEULYSPROTYRLYSARGTYRVAL
7   PHESERGLYTYRSERLYSASPPROLEUTHR
8   SERASNSERILEILEVALLYSILELYSALA
9   LYSGLUGLULYSTHRASPTYRLEUVALPRO
10   GLUGLNGLYTYRTHRLYSPHESERTYRGLU
11   PHEGLUTHRTHRGLULYSASPSERSERASN
12   ILEGLUILETHRLEUILEGLYSERGLYTHR
13   THRTYRLEUASPASNLEUSERILETHRGLU
14   LEUASNSERTHRPROGLU

Entity 2, CALCIUM ION - Ca - 40.078 Da.

1   CA

Samples:

sample_1: RBD1, [U-13C; U-15N], 0.5 mM; HEPES 15 mM; sodium chloride 150 mM; D2O 10%; Ca2+ 13 mM

sample_conditions_1: ionic strength: 0.189 M; pH: 7.0; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
2D 1H-15N HSQC TROSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection

NMRPipe v9.7, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CcpNMR v3.0.0, CCPN - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance III 950 MHz
  • Bruker Avance III 600 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts