BMRB Entry 50421

Title:
Detection of key sites of dimer dissociation and unfolding initiation during activation of acid-stress chaperone HdeA at low pH
Deposition date:
2020-07-31
Original release date:
2020-11-02
Authors:
Widjaja, Marlyn; Gomez, Jafaeth; Benson, Jonathon; Crowhurst, Karin
Citation:

Citation: Widjaja, Marlyn; Gomez, Jafaeth; Benson, Jonathon; Crowhurst, Karin. "Detection of key sites of dimer dissociation and unfolding initiation during activation of acid-stress chaperone HdeA at low pH"  Biochim. Biophys. Acta Proteins Proteom. 1869, 140576-140576 (2021).
PubMed: 33253897

Assembly members:

Assembly members:
entity_1, polymer, 89 residues, Formula weight is not available

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: pET21a

Entity Sequences (FASTA):

Data typeCount
13C chemical shifts663
15N chemical shifts250
1H chemical shifts400
T1 relaxation values322
T2 relaxation values322

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1HdeA dimer, chain 1, folded state1
2HdeA dimer, chain 2, folded state1
3HdeA monomer, conformer 1, unfolded state1
4HdeA monomer, conformer 2, unfolded state1

Entities:

Entity 1, HdeA dimer, chain 1, folded state 89 residues - Formula weight is not available

This is the sequence of the periplasmic protein (after removal of signal sequence)

1   ALAASPALAGLNLYSALAALAASPASNLYS
2   LYSPROVALASNSERTRPTHRCYSGLUASP
3   PHELEUALAVALASPGLUSERPHEGLNPRO
4   THRALAVALGLYPHEALAGLUALALEUASN
5   ASNLYSASPLYSPROGLUASPALAVALLEU
6   ASPVALGLNGLYILEALATHRVALTHRPRO
7   ALAILEVALGLNALACYSTHRGLNASPLYS
8   GLNALAASNPHELYSASPLYSVALLYSGLY
9   GLUTRPASPLYSILELYSLYSASPMET

Samples:

sample_1: HdeA, [U-13C; U-15N; U-2H], 1.0 mM; citrate 50 mM; DSS 2 mM; sodium azide 0.2 mM

sample_2: HdeA, [U-13C; U-15N], 1.0 mM; citrate 50 mM; DSS 2 mM; sodium azide 0.2 mM

sample_3: HdeA, [U-15N; 13C HD-Ile,Leu; HG-Val], 1.0 mM; citrate 50 mM; DSS 2 mM; sodium azide 0.2 mM

sample_conditions_1: ionic strength: 0.05 M; pH: 2.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.05 M; pH: 2.6; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 0.05 M; pH: 2.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_2
2D 1H-15N HSQCsample_2isotropicsample_conditions_3
T1/R1 relaxationsample_1isotropicsample_conditions_1
T1/R1 relaxationsample_2isotropicsample_conditions_2
T1/R1 relaxationsample_2isotropicsample_conditions_3
T2/R2 relaxationsample_1isotropicsample_conditions_1
T2/R2 relaxationsample_2isotropicsample_conditions_2
T2/R2 relaxationsample_2isotropicsample_conditions_3
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_2
2D 1H-13C HSQCsample_3isotropicsample_conditions_3
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_2
3D HNCACBsample_2isotropicsample_conditions_3
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_2
3D CBCA(CO)NHsample_2isotropicsample_conditions_3
3D HNCOsample_2isotropicsample_conditions_3
3D CCH-TOCSYsample_2isotropicsample_conditions_3
3D HCCH-TOCSYsample_2isotropicsample_conditions_3
3D (H)CCH-TOCSYsample_2isotropicsample_conditions_3
T1/R1 relaxationsample_3isotropicsample_conditions_2
T2/R2 relaxationsample_3isotropicsample_conditions_2
T1/R1 relaxationsample_3isotropicsample_conditions_3
T2/R2 relaxationsample_3isotropicsample_conditions_3

Software:

VNMRj 4.1 - collection

NMRPipe v2018.037.21.06 - processing

NMRViewJ v9.2.0-b2 - chemical shift assignment, data analysis

Shiftcor v1.0 - chemical shift calculation

NMR spectrometers:

  • Agilent DD2 600 MHz

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