BMRB Entry 30779

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30779
MolProbity Validation Chart

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Title:
NMR structure of the Streptococcus pyogenes NAD+-glycohydrolase translocation domain
Deposition date:
2020-07-22
Original release date:
2021-07-26
Authors:
Velarde, J.; Piai, A.; Chou, J.; Wessels, M.
Citation:

Citation: Velarde, Jorge; Piai, Alessandro; Lichtenstein, Ian; Lynskey, Nicola; Chou, James; Wessels, Michael. "Structure of the Streptococcus pyogenes NAD + Glycohydrolase Translocation Domain and Its Essential Role in Toxin Binding to Oropharyngeal Keratinocytes"  J. Bacteriol. 204, e0036621-e0036621 (2022).
PubMed: 34694903

Assembly members:

Assembly members:
entity_1, polymer, 159 residues, 17801.998 Da.

Natural source:

Natural source:   Common Name: Streptococcus pyogenes   Taxonomy ID: 1314   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Streptococcus pyogenes

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPVSGKENKKSDVKYETTKV MEANATSSKEDNHVMHTLDG SMSTVWEENSPGGGVGEVLS YKFASPMHIGRILIVNGDTS SKENYYKKNRIAKADVKYYN GNKLVLFQKIELGDTYTKKP HHIEIDKKLDVDRIDIEVTE VHQGQNKDILALSEVTFGN

Data sets:
Data typeCount
13C chemical shifts399
15N chemical shifts140
1H chemical shifts251

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 159 residues - 17801.998 Da.

1   GLYPROVALSERGLYLYSGLUASNLYSLYS
2   SERASPVALLYSTYRGLUTHRTHRLYSVAL
3   METGLUALAASNALATHRSERSERLYSGLU
4   ASPASNHISVALMETHISTHRLEUASPGLY
5   SERMETSERTHRVALTRPGLUGLUASNSER
6   PROGLYGLYGLYVALGLYGLUVALLEUSER
7   TYRLYSPHEALASERPROMETHISILEGLY
8   ARGILELEUILEVALASNGLYASPTHRSER
9   SERLYSGLUASNTYRTYRLYSLYSASNARG
10   ILEALALYSALAASPVALLYSTYRTYRASN
11   GLYASNLYSLEUVALLEUPHEGLNLYSILE
12   GLULEUGLYASPTHRTYRTHRLYSLYSPRO
13   HISHISILEGLUILEASPLYSLYSLEUASP
14   VALASPARGILEASPILEGLUVALTHRGLU
15   VALHISGLNGLYGLNASNLYSASPILELEU
16   ALALEUSERGLUVALTHRPHEGLYASN

Samples:

sample_1: NADase translocation domain, [U-13C; U-15N], 1 mM; MES 20 mM; NaCl 50 mM

sample_2: NADase translocation domain, [U-13C; U-15N; U-2H], 0.56 mM; MES 20 mM; NaCl 80 mM; EDTA 0.5 mM

sample_conditions_1: ionic strength: 50 mM; pH: 5.5; pressure: 1 .; temperature: 303 K

sample_conditions_2: ionic strength: 80 mM; pH: 5.5; pressure: 1 .; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
3D 15N-edited NOESY-TROSY-HSQCsample_1anisotropicsample_conditions_1
3D 13C-edited NOESYsample_1anisotropicsample_conditions_1
2D 1H-15N TROSY HSQCsample_2anisotropicsample_conditions_2
3D TROSY HNCAsample_2anisotropicsample_conditions_2
3D TROSY HNCACBsample_2anisotropicsample_conditions_2
3D TROSY HN(CA)COsample_2anisotropicsample_conditions_2
3D TROSY HNCOsample_2anisotropicsample_conditions_2
3D TROSY HN(CO)CAsample_2anisotropicsample_conditions_2

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

XEASY, Bartels et al. - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Sparky, Goddard - data analysis

TopSpin, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AVANCE III 800 MHz
  • Bruker AVANCE III HD 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks