BMRB Entry 30759

Name: Structure of a Stable Interstrand DNA Crosslink Involving an dA Amino Group and an Abasic Site
Published: 2021-05-03

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PDB ID: 6xah
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30759
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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:

Structure of a Stable Interstrand DNA Crosslink Involving an dA Amino Group and an Abasic Site

Deposition date:

2020-06-04

Original release date:

2021-05-03

Authors:

Kellum Jr., A.; Qiu, D.; Voehler, M.; Martin, W.; Gates, K.; Stone, M.

Citation:

Citation: Kellum Jr., A.; Qiu, D.; Voehler, M.; Martin, W.; Gates, K.; Stone, M.. "Structure of a Stable Interstrand DNA Cross-Link Involving a beta- N -Glycosyl Linkage Between an N 6 -dA Amino Group and an Abasic Site." Biochemistry 60, 41-52 (2021).
PubMed: 33382597

Assembly members:

Assembly members:
entity_1, polymer, 18 residues, 5480.576 Da.
entity_2, polymer, 18 residues, 5439.544 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):
entity_1: TATGTCTAAGTTCATCTA
entity_2: TAGATGAACXTAGACATA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	196

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

Entities:

Entity 1, unit_1 18 residues - 5480.576 Da.

1

DT

DA

DT

DG

DT

DC

DT

DA

DG

2

DT

DC

DA

DT

DC

DT

DA

Entity 2, unit_2 18 residues - 5439.544 Da.

1

DT

DA

DG

DA

DT

DG

DA

DC

AAB

2

DT

DA

DG

DA

DC

DA

DT

DA

Samples:

sample_1: deoxyribonucleic acid 500 ± 0.2 uM

sample_2: deoxyribonucleic acid 500 ± 0.2 uM

sample_conditions_1: ionic strength: 120 mM; pH: 8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 120 mM; pH: 8; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	anisotropic	sample_conditions_2
2D 1H-1H COSY	sample_1	anisotropic	sample_conditions_1

Software:

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

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

TopSpin, Bruker Biospin - data analysis, processing

NMR spectrometers:

Bruker AVANCE III 900 MHz