BMRB Entry 36045

Name: Solution structure of E.coli HdeA
Published: 2018-07-10

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PDB ID: 5wyo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36045
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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:

Solution structure of E.coli HdeA

Deposition date:

2017-01-14

Original release date:

2018-07-10

Authors:

Yang, C.; Hu, Y.; Jin, C.

Citation:

Citation: Yu, X.; Yang, C.; Ding, J.; Niu, X.; Hu, Y.; Jin, C.. "Characterizations of the Interactions between Escherichia coli Periplasmic Chaperone HdeA and Its Native Substrates during Acid Stress" Biochemistry 56, 5748-5757 (2017).
PubMed: 29016106

Assembly members:

Assembly members:
Acid stress chaperone HdeA, polymer, 89 residues, 9752.882 Da.

Natural source:

Natural source: Common Name: Escherichia coli O157:H7 Taxonomy ID: 83334 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia Escherichia coli

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Acid stress chaperone HdeA: ADAQKAADNKKPVNSWTCED FLAVDESFQPTAVGFAEALN NKDKPEDAVLDVQGIATVTP AIVQACTQDKQANFKDKVKG EWDKIKKDM

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	345
15N chemical shifts	92
1H chemical shifts	547

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	1

Entities:

Entity 1, entity_1 89 residues - 9752.882 Da.

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-99% 13C; U-99% 15N], 2.0 mM; sodium citrate 20 mM; sodium phosphate 20 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 180 mM; pH: 3.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 13C/15N-filtered 13C-edited NOESY	sample_1	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AvanceIII 600 MHz
Bruker AvanceIII 700 MHz
Bruker AvanceIII 800 MHz

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