BMRB Entry 18050

Name: Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch
Published: 2012-03-02

Click here to enlarge.

PDB ID: 2llj
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18050
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:

Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch

Deposition date:

2011-11-10

Original release date:

2012-03-02

Authors:

Jourdan, Muriel; Granzhan, Anton; Guillot, Regis; Dumy, Pascal; Teulade-Fichou, Marie-Paule

Citation:

Citation: Jourdan, Muriel; Granzhan, Anton; Guillot, Regis; Dumy, Pascal; Teulade-Fichou, Marie-Paule. "Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch." Nucleic Acids Res. 40, 5115-5128 (2012).
PubMed: 22362757

Assembly members:

Assembly members:
DNA_1, polymer, 11 residues, 3365.224 Da.
DNA_2, polymer, 11 residues, 3334.213 Da.
LLJ, non-polymer, 516.717 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_1: CGTCGTAGTGC
DNA_2: GCACTTCGACG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	179
31P chemical shifts	9

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_1	1
2	DNA_2	2
3	bis-naphthalene	3

Entities:

Entity 1, DNA_1 11 residues - 3365.224 Da.

1

DC

DG

DT

DC

DG

DT

DA

DG

DT

DG

2

DC

Entity 2, DNA_2 11 residues - 3334.213 Da.

1

DG

DC

DA

DC

DT

DC

DG

DA

DC

2

DG

Entity 3, bis-naphthalene - C32 H44 N4 O2 - 516.717 Da.

1

LLJ

Samples:

sample_1: DNA_1 1.5 mM; DNA_2 1.5 mM; 2_7-bisnaphthalene 1.5 mM; H2O 90%; D2O 10 *

sample_conditions_1: ionic strength: 0.06 M; pH: 6; pressure: 1 atm; temperature: 283 K

Experiments:

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

Software:

AMBER v10.1, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - structure solution

NMR spectrometers:

Varian UnityPlus 500 MHz
Varian Unity 800 MHz