BMRB Entry 25110

Name: Solution structure of a left-handed G-quadruplex
Published: 2015-02-16

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PDB ID: 2ms9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25110
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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:

Solution structure of a left-handed G-quadruplex

Deposition date:

2014-07-25

Original release date:

2015-02-16

Authors:

Chung, Wan Jun; Heddi, Brahim; Schmitt, Emmanuelle; Lim, Kah Wai; Mechulam, Yves; Phan, Anh Tuan

Citation:

Citation: Chung, Wan Jun; Heddi, Brahim; Schmitt, Emmanuelle; Lim, Kah Wai; Mechulam, Yves; Phan, Anh Tuan. "Structure of a left-handed DNA G-quadruplex" Proc. Natl. Acad. Sci. U. S. A. 112, 2729-2733 (2015).
PubMed: 25695967

Assembly members:

Assembly members:
DNA_(28-MER), polymer, 28 residues, 8872.726 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_(28-MER): TGGTGGTGGTGGTTGTGGTG GTGGTGTT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	267

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (28-MER)	1

Entities:

Entity 1, DNA (28-MER) 28 residues - 8872.726 Da.

1

DT

DG

DT

DG

DT

DG

DT

2

DG

DT

DG

DT

DG

DT

DG

3

DG

DT

DG

DT

DG

DT

Samples:

sample_1: DNA (28-MER)0.2 – 2 mM; DNA (28-MER), [U-2% 15N], 0.2 – 0.5 mM; DNA (28-MER), [U-100% 2H], 0.2 – 0.5 mM; H2O 90%; D2O 10%

sample_2: DNA (28-MER)0.2 – 2 mM; DNA (28-MER), [U-4% 13C; U-4% 15N], 0.2 – 1 mM; D2O 100%

sample_conditions_1: ionic strength: 90 mM; pH: 7; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H JR NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C JR HMBC	sample_1	isotropic	sample_conditions_1
15N-FILTERED	sample_1	isotropic	sample_conditions_1
D-LABELED	sample_1	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

TOPSPIN, Bruker Biospin - collection

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz