BMRB Entry 19572

Name: Solution NMR structure of quadruplex d(TGGGTTTGGGTTGGGTTTGGG) in sodium conditions.
Published: 2014-10-27

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PDB ID: 2mfu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19572
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2013-10-23

Original release date:

2014-10-27

Authors:

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

Citation:

Citation: Karsisiotis, Andreas Ioannis; Dillon, Paul; Webba da Silva, Mateus. "In preparation" .

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: TGGGTTTGGGTTGGGTTTGG G

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	180

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

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

Entities:

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

1

DT

DG

DT

DG

2

DT

DG

DT

DG

3

DG

Samples:

Exchangeable_protons_(278K): DNA (5'-D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3')5 – 6 mM; sodium phosphate 20 mM; sodium chloride 70 mM; H2O 93%; D2O, [U-100% 2H], 7%

Non_exchangeable_protons_(293K): DNA (5'-D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3')5 – 6 mM; sodium phosphate 20 mM; sodium chloride 70 mM; D2O, [U-100% 2H], 100%

Exchangeable_protons_(278K)_conditions: ionic strength: 95 mM; pH: 6.8; pressure: 1 atm; temperature: 278 K

Non_exchangeable_protons_(293K)_conditions: ionic strength: 95 mM; pH: 6.8; 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 DQF-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
2D 1H-13C HMBC (H1-H8 long range correlation)	Exchangeable_protons_(278K)	isotropic	Exchangeable_protons_(278K)_conditions

Software:

VNMRJ, Varian - collection

FELIX, Accelrys Software Inc. - chemical shift assignment, data analysis, processing

SPARKY, Goddard - chemical shift assignment, data analysis

Molmol, Koradi, Billeter and Wuthrich - data analysis

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

NMR spectrometers:

Varian VNMRS 500 500 MHz