BMRB Entry 30822

Name: Deoxyuridine in DNA Structure: Solution Structure of [d(CGUGAATTCGCG)]2
Published: 2021-12-10

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PDB ID: 7kwl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30822
MolProbity Validation Chart

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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:

Deoxyuridine in DNA Structure: Solution Structure of [d(CGUGAATTCGCG)]2

Deposition date:

2020-12-01

Original release date:

2021-12-10

Authors:

Meints, G.; Ljunggren, K.

Citation:

Citation: Westwood, M; Ljunggren, K; Boyd, Benjamin; Becker, Jaclyn; Dwyer, Tammy; Meints, Gary. "Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA" Biochemistry 60, 873-885 (2021).
PubMed: 33689312

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3584.397 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XGUGAATTCGCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	78

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	1

Entities:

Entity 1, unit_1 12 residues - 3584.397 Da.

1

DCZ

DG

DU

DG

DA

DT

DC

DG

2

DC

DG

Samples:

sample_1: DNA 1.0 mM

sample_conditions_1: ionic strength: 25 mM; pH: 7.4 pD; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1

Software:

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

Felix, Accelrys Software Inc. - chemical shift assignment, peak picking

NMR spectrometers:

Varian INOVA 400 MHz
Varian INOVA 500 MHz