BMRB Entry 34516

Name: Parallel 17-mer DNA G-quadruplex
Published: 2021-01-25

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PDB ID: 6yy4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34516
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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:

Parallel 17-mer DNA G-quadruplex

Deposition date:

2020-05-04

Original release date:

2021-01-25

Authors:

Srb, P.; Curtis, C.; Veverka, V.

Citation:

Citation: Volek, Martin; Kolesnikova, Sofia; Svehlova, Katerina; Srb, Pavel; Sgallova, Rachel; Streckerova, Tereza; Redondo, Juan; Veverka, Vaclav; Curtis, Edward. "Overlapping but distinct: a new model for G-quadruplex biochemical specificity" Nucleic Acids Res. 49, 1816-1827 (2021).
PubMed: 33544841

Assembly members:

Assembly members:
entity_1, polymer, 17 residues, 5453.519 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGGTGGGAAGGGTGGGA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	34
1H chemical shifts	119

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 17 residues - 5453.519 Da.

1

DG

DT

DG

DA

DG

2

DG

DT

DG

DA

Samples:

sample_1: 5'-D(*GP*GP*GP*TP*GP*GP*GP*AP*AP*GP*GP*GP*TP*GP*GP*GP*A)-3' 0.8 mM; TRIS, deuterated, 25 mM; potassium chloride 200 mM; magnesium chloride 1 mM

sample_conditions_1: ionic strength: 225 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D TOCSY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

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

Sparky, Goddard - chemical shift assignment

NMR spectrometers:

Bruker AVANCE 850 MHz