BMRB Entry 17562

Name: N2-dG:N2-dG interstrand cross-link induced by trans-4-hydroxynonenal
Published: 2012-04-02

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PDB ID: 2lbi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17562
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

N2-dG:N2-dG interstrand cross-link induced by trans-4-hydroxynonenal

Deposition date:

2011-03-31

Original release date:

2012-04-02

Authors:

Huang, Hai; Kozekov, Ivan; Wang, Hao; Kozekova, Albena; Rizzo, Carmelo; Stone, Michael

Citation:

Citation: Huang, Hai; Wang, Hao; Kozekova, Albena; Rizzo, Carmelo; Stone, Michael. "Formation of a N2-dG:N2-dG carbinolamine DNA cross-link by the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N2-dG adduct" J. Am. Chem. Soc. 133, 16101-16110 (2011).
PubMed: 21916419

Assembly members:

Assembly members:
DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'), polymer, 12 residues, 3663.422 Da.
DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3'), polymer, 12 residues, 3663.422 Da.
HNE, non-polymer, 156.224 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 (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'): GCTAGCGAGTCC
DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3'): GGACTCGCTAGC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	150

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(GPCPTPAPGPCPGPAPGPTPCPC)-3')	1
2	DNA (5'-D(GPGPAPCPTPCPGPCPTPAPGPC)-3')	2
3	(2E,4R)-4-HYDROXYNON-2-ENAL	3

Entities:

Entity 1, DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') 12 residues - 3663.422 Da.

1

DG

DC

DT

DA

DG

DC

DG

DA

DG

DT

2

DC

Entity 2, DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3') 12 residues - 3663.422 Da.

1

DG

DA

DC

DT

DC

DG

DC

DT

DA

2

DG

DC

Entity 3, (2E,4R)-4-HYDROXYNON-2-ENAL - C9 H16 O2 - 156.224 Da.

1

HNE

Samples:

sample_1: DNA_1 1 mM; DNA_2 1 mM; (2E,4R)-4-HYDROXYNON-2-ENAL 1 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.3; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 800 MHz