BMRB Entry 5730

Click here to enlarge.

PDB ID: 1n8c
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR5730
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

1H Chemical Shift Assignments for a DNA Duplex with N6-Deoxyadenosine Adduct of (9S,10R)-9,10-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene

Deposition date:

2003-03-11

Original release date:

2003-05-19

Authors:

Volk, D.; Thiviyanathan, V.; Rice, J.; Luxon, B.; Shah, J.; Yagi, H.; Sayer, J.; Yeh, H.; Jerina, D.; Gorenstein, D.

Citation:

Citation: Volk, David; Thiviyanathan, Varatharasa; Rice, Jeffrey; Luxon, Bruce; Shah, Jamshed; Yagi, Haruhiko; Sayer, Jane; Yeh, Herman; Jerina, Donald; Gorenstein, David. "Solution Structure of a Cis-Opened (10R)-N6-Deoxyadenosine Adduct of (9S,10R)-(9,10)-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex" Biochemistry 42, 1410-1420 (2003).
PubMed: 12578353

Assembly members:

Assembly members:
Benzo[a]pyrene adducted DNA duplex, polymer, 11 residues, Formula weight is not available
Benzo[a]pyrene adducted DNA duplex, polymer, 11 residues, Formula weight is not available
1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, non-polymer, 304.339 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: Eukaryota Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Benzo[a]pyrene adducted DNA duplex: CGGTCACGAGG
Benzo[a]pyrene adducted DNA duplex: CCTCGTGACCG

Data sets:

assigned_chemical_shifts

Data type	Count
1H chemical shifts	234

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Strand1	1
2	Strand2	2
3	7,8,9,10-tetrahydro benzo[a]pyrene	3

Entities:

Entity 1, Strand1 11 residues - Formula weight is not available

1

DC

DG

DT

DC

DA

DC

DG

DA

DG

2

DG

Entity 2, Strand2 11 residues - Formula weight is not available

1

DC

DT

DC

DG

DT

DG

DA

DC

2

DG

Entity 3, 7,8,9,10-tetrahydro benzo[a]pyrene - C20 H16 O3 - 304.339 Da.

1

BAP

Samples:

sample_1: Benzo[a]pyrene adducted DNA duplex 1.5 mM; Benzo[a]pyrene adducted DNA duplex 1.5 mM; (-)-7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE 1.5 mM; Phosphates 20 mM; NaCl 57 mM; sodium azide 0.5 mM; H2O 90%; D2O 10%

sample_2: Benzo[a]pyrene adducted DNA duplex 1.5 mM; Benzo[a]pyrene adducted DNA duplex 1.5 mM; (-)-7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE 1.5 mM; Phosphates 20 mM; NaCl 57 mM; sodium azide 0.5 mM; D2O 99.96%

sample_cond_1: ionic strength: 100 mM; pH: 6.7; pressure: 1 atm; temperature: 278 K

sample_cond_2: ionic strength: 100 mM; pH*: 6.7; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	not available	not available	not available
2D TOCSY	not available	not available	not available
2D ROESY	not available	not available	not available
Exchange-Only	not available	not available	not available

Software:

VNMR v6.1 - collection, data analysis

MORASS v2.51 - iterative matrix relaxation

AMBER v5.0, 6.0, and 7.0 - refinement

NMR spectrometers:

Varian UNITYplus 600 MHz
Varian Unityplus 750 MHz