BMRB Entry 18209

Name: Solution-state structure of an intramolecular G-quadruplex w th propeller, diagonal and edgewise loops
Published: 2012-05-08

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PDB ID: 2lod
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18209
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution-state structure of an intramolecular G-quadruplex w th propeller, diagonal and edgewise loops

Deposition date:

2012-01-23

Original release date:

2012-05-08

Authors:

Marusic, Maja; Sket, Primoz; Bauer, Lubos; Viglasky, Viktor; Plavec, Janez

Citation:

Citation: Marusic, Maja; Sket, Primoz; Bauer, Lubos; Viglasky, Viktor; Plavec, Janez. "Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops." Nucleic Acids Res. 40, 6946-6956 (2012).
PubMed: 22532609

Assembly members:

Assembly members:
DNA_molecule_G3ATG3ACACAG4ACG3, polymer, 22 residues, 6972.544 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_molecule_G3ATG3ACACAG4ACG3: GGGATGGGACACAGGGGACG GG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	153

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_molecule_G3ATG3ACACAG4ACG3	1

Entities:

Entity 1, DNA_molecule_G3ATG3ACACAG4ACG3 22 residues - 6972.544 Da.

1

DG

DA

DT

DG

DA

DC

2

DA

DC

DA

DG

DA

DC

DG

3

DG

Samples:

sample_1: potassium phosphate 10 mM; potassium chloride 40 mM; H2O 90%; D2O 10%; DNA_molecule_G3ATG3ACACAG4ACG3 1.7 mM

sample_2: potassium phosphate 10 mM; potassium chloride 40 mM; D2O 100%; DNA_molecule_G3ATG3ACACAG4ACG3 2.3 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.8; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1

Software:

VNMRJ, Varian - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, peak picking

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement, structure solution

NMR spectrometers:

Varian Uniform NMR System 800 MHz