BMRB Entry 34292

Name: The CTD of HpDprA, a DNA binding Winged Helix domain which do not bind dsDNA
Published: 2019-04-22

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PDB ID: 6gw7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34292
MolProbity Validation Chart

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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: The CTD of HpDprA, a DNA binding Winged Helix domain which do not bind dsDNA PubMed: 30771270

Deposition date: 2018-06-22 Original release date: 2019-04-22

Authors: Lisboa, J.; Celma, L.; Sanchez, D.; Marquis, M.; Andreani, J.; Guerois, R.; Ochsenbein, F.; Durand, D.; Marsin, S.; Cuniasse, P.; Radicella, J.; Quevillon-Cheruel, S.

Citation: Lisboa, J.; Celma, L.; Sanchez, D.; Marquis, M.; Andreani, J.; Guerois, R.; Ochsenbein, F.; Durand, D.; Marsin, S.; Cuniasse, P.; Radicella, J.; Quevillon-Cheruel, S.. "The C-terminal domain of HpDprA is a DNA-binding winged helix domain that does not bind double-stranded DNA." FEBS J. 286, 1941-1958 (2019).

Assembly members:
entity_1, polymer, 59 residues, 7139.292 Da.

Natural source: Common Name: Campylobacter pylori Taxonomy ID: 210 Superkingdom: Bacteria Kingdom: not available Genus/species: Helicobacter pylori

Experimental source: Production method: recombinant technology Host organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Entity Sequences (FASTA):
entity_1: MLKDYHLKEMPEMEDEFLEY CAKNPSYEEAYLKFGDKLLE YELLGKIKRINHIVVLAHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	221
15N chemical shifts	55
1H chemical shifts	427

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 59 residues - 7139.292 Da.

1

MET

LEU

LYS

ASP

TYR

HIS

LEU

LYS

GLU

MET

2

PRO

GLU

MET

GLU

ASP

GLU

PHE

LEU

GLU

TYR

3

CYS

ALA

LYS

ASN

PRO

SER

TYR

GLU

ALA

4

TYR

LEU

LYS

PHE

GLY

ASP

LYS

LEU

GLU

5

TYR

GLU

LEU

GLY

LYS

ILE

LYS

ARG

ILE

6

ASN

HIS

ILE

VAL

LEU

ALA

HIS

Samples:

sample_1: HpDprA CTD, [U-15N; U-13C], 128 uM; Phosphate Buffer (NH2PO4) 20 mM; NaCl 50 mM

sample_2: HpDprA CTD, [U-13C; U-15N], 128 uM; Phosphate Buffer (NH2PO4) 20 mM; NaCl 50 mM

sample_3: HpDprA CTD, [U-15N], 34 uM; Phosphate Buffer (NH2PO4) 20 mM; NaCl 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 5.6; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 50 mM; pH: 5.6 pD; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 50 mM; pH: 7.4; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_3
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment

CcpNMR, CCPN - data analysis

CANDID, Herrmann, Guntert and Wuthrich - structure calculation

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

NMR spectrometers:

Bruker Avance 950 MHz
Bruker DRX 600 MHz

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