BMRB Entry 18781

Name: DNA duplex containing mispair-aligned O6G-heptylene-O6G interstrand cross-link
Published: 2013-10-14

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PDB ID: 2lzw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18781
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:

DNA duplex containing mispair-aligned O6G-heptylene-O6G interstrand cross-link

Deposition date:

2012-10-11

Original release date:

2013-10-14

Authors:

Denisov, Alexey; McManus, Francis; Noronha, Anne; Wilds, Christopher

Citation:

Citation: Denisov, Alexey; McManus, Francis; O'Flaherty, Derek; Noronha, Anne; Wilds, Christopher. "Solution structures of DNA duplexes containing mispair-aligned O4U-heptylene-O4U and O6G-heptylene-O6G interstrand cross-links" Biochemistry ., .-..

Assembly members:

Assembly members:
DNA, polymer, 11 residues, 3373.250 Da.
HEPTANE, non-polymer, 100.202 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: CGAAAGTTTCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	88

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_1	1
2	DNA_2	1
3	HEPTANE	2

Entities:

Entity 1, DNA_1 11 residues - 3373.250 Da.

1

DC

DG

DA

DG

DT

DC

2

DG

Entity 2, HEPTANE - C7 H16 - 100.202 Da.

1

HP6

Samples:

sample_1: DNA 1 mM; D2O 100%

sample_2: DNA 1 mM; D2O 10%; H2O 90%

sample_conditions_1: ionic strength: 0.1 M; pH: 7.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.1 M; pH: 7.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-31P HSQC	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_2

Software:

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

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

NMRView, Johnson, One Moon Scientific - data analysis

VNMRJ, Varian - collection

NMR spectrometers:

Varian Unity Inova 500 MHz
Varian Unity Inova 800 MHz
Varian VNMRS 500 MHz