BMRB Entry 36022

Name: Structure of two TTTA repeats
Published: 2016-11-03

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PDB ID: 5gwq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36022
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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 two TTTA repeats

Deposition date:

2016-09-13

Original release date:

2016-11-03

Authors:

Guo, Pei; Lam, Sik Lok

Citation:

Citation: Guo, Pei; Lam, Sik Lok. "Minidumbbell: A New Form of Native DNA Structure" J. Am. Chem. Soc. 138, 12534-12540 (2016).
PubMed: 27589409

Assembly members:

Assembly members:
DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3'), polymer, 8 residues, 2406.613 Da.
SODIUM ION, non-polymer, 22.990 Da.

Natural source:

Natural source: Common Name: Staphylococcus aureus Taxonomy ID: 1280 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3'): TTTATTTA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	90

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_NA	2
3	entity_NA	2
4	entity_NA	2
5	entity_NA	2
6	entity_NA	2
7	entity_NA	2
8	entity_NA	2

Entities:

Entity 1, entity_1 8 residues - 2406.613 Da.

1

DT

DA

DT

DA

Entity 2, entity_NA - Na - 22.990 Da.

1

NA

Samples:

sample_1: DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3') 1.0 mM; DSS 0.1 mM; sodium phosphate 10 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 20 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

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

Software:

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

TOPSPIN, Bruker Biospin - processing

NMR spectrometers:

Bruker AvanceIII 700 MHz
Bruker AvanceII 500 MHz