BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 34352

Title: Solution NMR ensemble for a chimeric KH-S1 domain construct of exosomal polynucleotide phosphrylase at 298K compiled using the CoMAND method   PubMed: 30930065

Deposition date: 2019-01-14 Original release date: 2019-10-03

Authors: ElGamacy, M.; Truffault, V.; Zhu, H.; Coles, M.

Citation: ElGamacy, M.; Riss, M.; Zhu, H.; Truffault, V.; Coles, M.. "Mapping Local Conformational Landscapes of Proteins in Solution."  Structure 27, 853-865 (2019).

Assembly members:
entity_1, polymer, 171 residues, 18396.865 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 409438   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

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

Entity Sequences (FASTA):
entity_1: GAMGRGDISEFAPRIHTIKI NPDKIKDVIGKGGSVIRALT EETGTTIEIEDDGTVKIAAT DGEKAKHAIRRIEEITAEIE VGRVYTGKVTRIVDFGAFVA IGGGKEGLVHISQIADKRVE KVTDYLQMGQEVPVKVLEVD RQGRIRLSIKEATEQSQPAA APEAPAAEQGE

Data sets:
Data typeCount
13C chemical shifts599
15N chemical shifts133
1H chemical shifts708

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 171 residues - 18396.865 Da.

1   GLYALAMETGLYARGGLYASPILESERGLU
2   PHEALAPROARGILEHISTHRILELYSILE
3   ASNPROASPLYSILELYSASPVALILEGLY
4   LYSGLYGLYSERVALILEARGALALEUTHR
5   GLUGLUTHRGLYTHRTHRILEGLUILEGLU
6   ASPASPGLYTHRVALLYSILEALAALATHR
7   ASPGLYGLULYSALALYSHISALAILEARG
8   ARGILEGLUGLUILETHRALAGLUILEGLU
9   VALGLYARGVALTYRTHRGLYLYSVALTHR
10   ARGILEVALASPPHEGLYALAPHEVALALA
11   ILEGLYGLYGLYLYSGLUGLYLEUVALHIS
12   ILESERGLNILEALAASPLYSARGVALGLU
13   LYSVALTHRASPTYRLEUGLNMETGLYGLN
14   GLUVALPROVALLYSVALLEUGLUVALASP
15   ARGGLNGLYARGILEARGLEUSERILELYS
16   GLUALATHRGLUGLNSERGLNPROALAALA
17   ALAPROGLUALAPROALAALAGLUGLNGLY
18   GLU

Samples:

sample_1: KH-S1, [U-99% 13C; U-99% 15N], 1.6 mM; potassium phosphate 50 mM; sodium chloride 125 mM; HOPES buffer 25 mM

sample_conditions_1: ionic strength: 125 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D CNH-NOESYsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

Sparky, Goddard - chemical shift assignment

Shine, Riss & Coles - structure calculation

Rosetta v3.6, Das & Baker - structure calculation

NAMD v2.12, University of Illinois - refinement

CoMAND, in house - refinement

NMR spectrometers:

  • Bruker AvanceIII 600 MHz
  • Bruker AvanceIII 800 MHz

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