BMRB Entry 50421

Name: Detection of key sites of dimer dissociation and unfolding initiation during activation of acid-stress chaperone HdeA at low pH
Published: 2020-11-02

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50421

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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):

Entity Sequences (FASTA):
entity_1: ADAQKAADNKKPVNSWTCED FLAVDESFQPTAVGFAEALN NKDKPEDAVLDVQGIATVTP AIVQACTQDKQANFKDKVKG EWDKIKKDM

Data sets:

Data type	Count
13C chemical shifts	663
15N chemical shifts	250
1H chemical shifts	400
T1 relaxation values	322
T2 relaxation values	322

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HdeA dimer, chain 1, folded state	1
2	HdeA dimer, chain 2, folded state	1
3	HdeA monomer, conformer 1, unfolded state	1
4	HdeA monomer, conformer 2, unfolded state	1

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

ALA

ASP

ALA

GLN

LYS

ALA

ASP

ASN

LYS

2

LYS

PRO

VAL

ASN

SER

TRP

THR

CYS

GLU

ASP

3

PHE

LEU

ALA

VAL

ASP

GLU

SER

PHE

GLN

PRO

4

THR

ALA

VAL

GLY

PHE

ALA

GLU

ALA

LEU

ASN

5

ASN

LYS

ASP

LYS

PRO

GLU

ASP

ALA

VAL

LEU

6

ASP

VAL

GLN

GLY

ILE

ALA

THR

VAL

THR

PRO

7

ALA

ILE

VAL

GLN

ALA

CYS

THR

GLN

ASP

LYS

8

GLN

ALA

ASN

PHE

LYS

ASP

LYS

VAL

LYS

GLY

9

GLU

TRP

ASP

LYS

ILE

LYS

ASP

MET

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_3
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_2	isotropic	sample_conditions_2
T1/R1 relaxation	sample_2	isotropic	sample_conditions_3
T2/R2 relaxation	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation	sample_2	isotropic	sample_conditions_2
T2/R2 relaxation	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_3
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_2
3D HNCACB	sample_2	isotropic	sample_conditions_3
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_2
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_3
3D HNCO	sample_2	isotropic	sample_conditions_3
3D CCH-TOCSY	sample_2	isotropic	sample_conditions_3
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_3
3D (H)CCH-TOCSY	sample_2	isotropic	sample_conditions_3
T1/R1 relaxation	sample_3	isotropic	sample_conditions_2
T2/R2 relaxation	sample_3	isotropic	sample_conditions_2
T1/R1 relaxation	sample_3	isotropic	sample_conditions_3
T2/R2 relaxation	sample_3	isotropic	sample_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