BMRB Entry 19571

Name: Solution NMR structure of the d(GGGTTTTGGGTGGGTTTTGGG) quadruplex in sodium conditions.
Published: 2014-10-20

Click here to enlarge.

PDB ID: 2mft
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19571
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:

Solution NMR structure of the d(GGGTTTTGGGTGGGTTTTGGG) quadruplex in sodium conditions.

Deposition date:

2013-10-22

Original release date:

2014-10-20

Authors:

Karsisiotis, Andreas Ioannis; Webba da Silva, Mateus; Karsisiotis, Andreas Ioannis

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, polymer, 21 residues, 6643.305 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available 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: GGGTTTTGGGTGGGTTTTGG G

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
1H chemical shifts	345

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(GPGPGPTPTPTPTPGPGPGPTPGPGPGPTPTPTPTPGPGP*G)-3')	1

Entities:

Entity 1, DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 21 residues - 6643.305 Da.

1

DG

DT

DG

2

DT

DG

DT

DG

3

DG

Samples:

Exchangeable_Protons_(278K): DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 2 mM; sodium phosphate 20 mM; H2O 93%; D2O, [U-100% 2H], 7%

Non_exchangeable_Protons_(293K): DNA (5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*G)-3') 2 mM; sodium phosphate 20 mM; D2O, [U-100% 2H], 100%

Exchangeable_Protons_(278K)_conditions: ionic strength: 20 mM; pH: 7.8; pressure: 1 atm; temperature: 278 K

Non_exchangeable_Protons_(293K)_conditions: ionic strength: 20 mM; pH: 7.8; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	Non_exchangeable_Protons_(293K)	isotropic	Non_exchangeable_Protons_(293K)_conditions
2D 1H-1H COSY	Non_exchangeable_Protons_(293K)	isotropic	Non_exchangeable_Protons_(293K)_conditions
2D 1H-1H NOESY	Non_exchangeable_Protons_(293K)	isotropic	Non_exchangeable_Protons_(293K)_conditions
2D 1H-1H NOESY	Exchangeable_Protons_(278K)	isotropic	Exchangeable_Protons_(278K)_conditions
2D 1H-31P HSQC	Non_exchangeable_Protons_(293K)	isotropic	Non_exchangeable_Protons_(293K)_conditions

Software:

FELIX, Accelrys Software Inc. - processing

VNMRJ, Varian - collection

SPARKY, Goddard - chemical shift assignment, data analysis

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

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Varian VNMRS 500 500 MHz