BMRB Entry 53206

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR53206

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Title:
Active Site Protonation States in Avibactam-Bound Toho-1 b-Lactamase Revealed by NMR Crystallography
Deposition date:
2025-05-27
Original release date:
2026-10-20
Authors:
Williams, Christopher; Wang, Songlin; Thome, Alexander; Coates, Leighton; Rienstra, Chad; Mueller, Leonard
Citation:

Citation: Williams, Christopher; Wang, Songlin; Carta, Veronica; Langan, Patricia; Thome, Alexander; Ramos, Sebastian; Holmes, Jacob; Ghosh, Rittik; Weiss, Kevin; Beran, Gregory; Hartman, Joshua; Coates, Leighton; Rienstra, Chad; Mueller, Leonard. "NMR crystallography reveals active-site protonation states of Toho-1 b-lactamase in complex with avibactam "  Proc. Natl. Acad. Sci. U. S. A. 123, e2616547123-e2616547123 (2026).
PubMed: 42743273

Assembly members:

Assembly members:
entity_1, polymer, 261 residues, Formula weight is not available
entity_NXL, non-polymer, 267.260 Da.

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pJexpress401

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: NSVQQQLEALEKSSGGRLGV ALINTADNSQILYRADERFA MCSTSKVMAAAAVLKQSESD KHLLNQRVEIKKSDLVNYNP IAEKHVNGTMTLAELGAAAL QYSDNTAMNKLIAHLGGPDK VTAFARSLGDETFRLDRTEP TLNTAIPGDPRDTTTPLAMA QTLKNLTLGKALAETQRAQL VTWLKGNTTGSASIRAGLPK SWVVGDKTGSGDYGTTNDIA VIWPENHAPLVLVTYFTQPE QKAENRNDILAAAAKIVTHG F

Data sets:
Data typeCount
13C chemical shifts1150
15N chemical shifts313
1H chemical shifts3

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1
2ligand2

Entities:

Entity 1, entity 261 residues - Formula weight is not available

1   ASNSERVALGLNGLNGLNLEUGLUALALEU
2   GLULYSSERSERGLYGLYARGLEUGLYVAL
3   ALALEUILEASNTHRALAASPASNSERGLN
4   ILELEUTYRARGALAASPGLUARGPHEALA
5   METCYSSERTHRSERLYSVALMETALAALA
6   ALAALAVALLEULYSGLNSERGLUSERASP
7   LYSHISLEULEUASNGLNARGVALGLUILE
8   LYSLYSSERASPLEUVALASNTYRASNPRO
9   ILEALAGLULYSHISVALASNGLYTHRMET
10   THRLEUALAGLULEUGLYALAALAALALEU
11   GLNTYRSERASPASNTHRALAMETASNLYS
12   LEUILEALAHISLEUGLYGLYPROASPLYS
13   VALTHRALAPHEALAARGSERLEUGLYASP
14   GLUTHRPHEARGLEUASPARGTHRGLUPRO
15   THRLEUASNTHRALAILEPROGLYASPPRO
16   ARGASPTHRTHRTHRPROLEUALAMETALA
17   GLNTHRLEULYSASNLEUTHRLEUGLYLYS
18   ALALEUALAGLUTHRGLNARGALAGLNLEU
19   VALTHRTRPLEULYSGLYASNTHRTHRGLY
20   SERALASERILEARGALAGLYLEUPROLYS
21   SERTRPVALVALGLYASPLYSTHRGLYSER
22   GLYASPTYRGLYTHRTHRASNASPILEALA
23   VALILETRPPROGLUASNHISALAPROLEU
24   VALLEUVALTHRTYRPHETHRGLNPROGLU
25   GLNLYSALAGLUASNARGASNASPILELEU
26   ALAALAALAALALYSILEVALTHRHISGLY
27   PHE

Entity 2, ligand - C7 H13 N3 O6 S - 267.260 Da.

1   NXL

Samples:

sample_1: Toho-1 Beta-lactamase, [U-100% 13C; U-100% 15N], 350 mg/mL; PEG-8K 15%; Spermine 7 mM; MES 20 mM; Sodium Hydroxide 0.01 M; Avibactam 7 mM

sample_conditions_1: pH: 6.5; temperature: 263 K

Experiments:

NameSampleSample stateSample conditions
2D 13C-detected NCAsample_1isotropicsample_conditions_1
2D 13C-detected NCOsample_1isotropicsample_conditions_1
3D 13C-detected NCACXsample_1isotropicsample_conditions_1
3D 13C-detected NCOCXsample_1isotropicsample_conditions_1
2D 13C-detected CANCOsample_1isotropicsample_conditions_1
3D 13C-detected CC DARRsample_1isotropicsample_conditions_1
3D 13C-detected CC CORDsample_1isotropicsample_conditions_1
3D NCAcxNZsample_1isotropicsample_conditions_1
3D NCACX 200ms CC DARRsample_1isotropicsample_conditions_1
3D NCOCX 200ms CC DARRsample_1isotropicsample_conditions_1

Software:

CcpNMR v3.2 - chemical shift assignment, peak picking

TOPSPIN - processing

NMR spectrometers:

  • Bruker NEO 1100 MHz
  • Bruker AVANCE III 900 MHz
  • Varian VNMRS 600 MHz
  • Bruker AvNeo 600 600 MHz