BMRB Entry 30045

Name: DIY G-Quadruplexes: Solution structure of d(GGGTTTGGGTTTTGGGAGGG) in sodium
Published: 2017-03-30

Click here to enlarge.

PDB ID: 5j05
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30045
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

DIY G-Quadruplexes: Solution structure of d(GGGTTTGGGTTTTGGGAGGG) in sodium

Deposition date:

2016-03-27

Original release date:

2017-03-30

Authors:

Dvorkin, S.; Karsisiotis, A.; Webba da Silva, M.

Citation:

Citation: Dvorkin, Scarlett; Karsisiotis, Andreas; Webba da Silva, Mateus. "Encoding canonical DNA quadruplex structure." Sci Adv 4, eaat3007-eaat3007 (2018).
PubMed: 30182059

Assembly members:

Assembly members:
DNA (5'-D(*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), polymer, 20 residues, 6348.070 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'): GGGTTTGGGTTTTGGGAGGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	210

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 20 residues - 6348.070 Da.

1		DG	DG	DG	DT	DT	DT	DG	DG	DG	DT
2		DT	DT	DT	DG	DG	DG	DA	DG	DG	DG

Samples:

sample_1: DNA, none, 1 ± 1.0 mM; H2O 93%; D2O 7%

sample_2: DNA, none, 1 ± 1 mM; D2O 100%

sample_conditions_1: ionic strength: 20 mM; pH: 6.8 pD; pressure: 1 atm; temperature: 293.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
H,H jr-NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

Felix, Accelrys Software Inc. - chemical shift assignment, refinement

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

Varian VNMRS 500 MHz