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 52318

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52318

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Title: 1H, 13C, and 15N backbone resonance assignments of E. coli Peptide Deformylase (1-147) bound to 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide   PubMed: 38574272

Deposition date: 2024-02-09 Original release date: 2024-07-22

Authors: Kirschner, Hendrik; Heister, Nicole; Stoll, Raphael

Citation: Kirschner, Hendrik; Heister, Nicole; Zouatom, Manuela; Zhou, Tianyi; Hofmann, Eckhard; Scherkenbeck, Jurgen; Stoll, Raphael. "Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase"  J. Med. Chem. 67, 6384-6396 (2024).

Assembly members:
entity_1, polymer, 150 residues, Formula weight is not available
entity_BB4, non-polymer, 269.095 Da.

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: modified pET19

Entity Sequences (FASTA):
entity_1: GHMSVLQVLHIPDERLRKVA KPVEEVNAEIQRIVDDMFET MYAEEGIGLAATQVDIHQRI IVIDVSENRDERLVLINPEL LEKSGETGIEEGCLSIPEQR ALVPRAEKVKIRALDRDGKP FELEADGLLAICIQHEMDHL VGKLFMDYLS

Data sets:
Data typeCount
13C chemical shifts135
15N chemical shifts32
1H chemical shifts32

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Peptide Deformylase1
2ligand, BB42

Entities:

Entity 1, Peptide Deformylase 150 residues - Formula weight is not available

1   GLYHISMETSERVALLEUGLNVALLEUHIS
2   ILEPROASPGLUARGLEUARGLYSVALALA
3   LYSPROVALGLUGLUVALASNALAGLUILE
4   GLNARGILEVALASPASPMETPHEGLUTHR
5   METTYRALAGLUGLUGLYILEGLYLEUALA
6   ALATHRGLNVALASPILEHISGLNARGILE
7   ILEVALILEASPVALSERGLUASNARGASP
8   GLUARGLEUVALLEUILEASNPROGLULEU
9   LEUGLULYSSERGLYGLUTHRGLYILEGLU
10   GLUGLYCYSLEUSERILEPROGLUGLNARG
11   ALALEUVALPROARGALAGLULYSVALLYS
12   ILEARGALALEUASPARGASPGLYLYSPRO
13   PHEGLULEUGLUALAASPGLYLEULEUALA
14   ILECYSILEGLNHISGLUMETASPHISLEU
15   VALGLYLYSLEUPHEMETASPTYRLEUSER

Entity 2, ligand, BB4 - C10 H9 Br N2 O2 - 269.095 Da.

1   BB4

Samples:

sample_1: Peptide Deformylase, [U-15N], 0.45 mM; Peptide Deformylase, [U-13C; U-15N], 0.45 mM; KH2PO4 20 mM

sample_conditions_1: ionic strength: 0.052 M; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
1D 1Hsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
1D 1Hsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACOsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1

Software:

CcpNMR v2.5.2 - chemical shift assignment

NMR spectrometers:

  • Bruker AVANCE NEO 600 MHz
  • Bruker AVANCE III 700 MHz

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