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 30611

Title: NMR solution structure of YfiD   PubMed: 31250200

Deposition date: 2019-05-10 Original release date: 2019-07-05

Authors: Bowman, S.; Drennan, C.

Citation: Bowman, S.; Backman, L.; Bjork, R.; Andorfer, M.; Yori, S.; Caruso, A.; Stultz, C.; Drennan, C.. "Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme."  J. Biol. Inorg. Chem. ., .-. (2019).

Assembly members:
entity_1, polymer, 127 residues, 14286.153 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

Entity Sequences (FASTA):
entity_1: MITGIQITKAANDDLLNSFW LLDSEKGEARCIVAKAGFAE DEVVAVSKLGDIEYREVPVE VKPEVRVEGGQHLNVNVLRR ETLEDAVKHPEKYPQLTIRV SGYAVRFNSLTPEQQRDVIA RTFTESL

Data sets:
Data typeCount
13C chemical shifts76
15N chemical shifts57
1H chemical shifts349

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 127 residues - 14286.153 Da.

1   METILETHRGLYILEGLNILETHRLYSALA
2   ALAASNASPASPLEULEUASNSERPHETRP
3   LEULEUASPSERGLULYSGLYGLUALAARG
4   CYSILEVALALALYSALAGLYPHEALAGLU
5   ASPGLUVALVALALAVALSERLYSLEUGLY
6   ASPILEGLUTYRARGGLUVALPROVALGLU
7   VALLYSPROGLUVALARGVALGLUGLYGLY
8   GLNHISLEUASNVALASNVALLEUARGARG
9   GLUTHRLEUGLUASPALAVALLYSHISPRO
10   GLULYSTYRPROGLNLEUTHRILEARGVAL
11   SERGLYTYRALAVALARGPHEASNSERLEU
12   THRPROGLUGLNGLNARGASPVALILEALA
13   ARGTHRPHETHRGLUSERLEU

Samples:

sample_1: YfiD, [U-15N], 0.7 mM; HEPES 18 mM; ammonium sulfate 2.7 mM; D2O 10 % v/v

sample_2: YfiD, [U-100% 13C; U-100% 15N], 1.3 mM; HEPES 18 mM; ammonium sulfate 2.7 mM; D2O 10 % v/v

sample_conditions_1: ionic strength: 2.7 mM; pH: 7.2; pressure: 760 mmHg; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1

Software:

VNMR, Varian - collection

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

Sparky, Goddard - chemical shift assignment, peak picking, structure calculation

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

NMR spectrometers:

  • Varian INOVA 800 MHz
  • FBML CMR 600 E 600 MHz

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