BMRB Entry 36379

Name: NMR solution structures of the DNA minidumbbell formed by two CmCTG repeats at pH 5
Published: 2021-08-02

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PDB ID: 7d0y
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36379
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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:

NMR solution structures of the DNA minidumbbell formed by two CmCTG repeats at pH 5

Deposition date:

2020-09-12

Original release date:

2021-08-02

Authors:

Wan, L.; Guo, P.; Lam, S.

Citation:

Citation: Wan, Liqi; Yi, Jie; Lam, Sik; Lee, Hung; Guo, Pei. "5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbell" Chemistry 27, 6740-6747 (2021).
PubMed: 33501691

Assembly members:

Assembly members:
DNA (5'-D(*(DCZ)P*(5CM)P*TP*GP*CP*(5CM)P*TP*G)-3'), polymer, 8 residues, 2326.641 Da.
SODIUM ION, non-polymer, 22.990 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*(DCZ)P*(5CM)P*TP*GP*CP*(5CM)P*TP*G)-3'): XXTGCXTG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
1H chemical shifts	85

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	2
4	unit_4	2
5	unit_5	2
6	unit_6	2

Entities:

Entity 1, unit_1 8 residues - 2326.641 Da.

1

DCZ

5CM

DT

DG

DC

5CM

DT

DG

Entity 2, unit_2 - Na - 22.990 Da.

1

NA

Samples:

sample_1: DNA 0.2 ± 0.02 mM; DSS 0.02 ± 0.005 mM; NaCl 10 ± 1 mM; D2O, [U-2H], 99.96%

sample_conditions_1: ionic strength: 10 mM; pH: 5; 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 COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

TopSpin, Bruker Biospin - chemical shift assignment

NMR spectrometers:

Bruker AVANCE 700 MHz
Bruker AVANCE 500 MHz