BMRB Entry 34587

Name: deoxyxylose nucleic acid hairpin
Published: 2021-02-05

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PDB ID: 7bfs
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34587
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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:

deoxyxylose nucleic acid hairpin

Deposition date:

2021-01-04

Original release date:

2021-02-05

Authors:

Mattelaer, C.; Mohitosh, M.; Smets, L.; Maiti, M.; Schepers, G.; Mattelaer, H.; Rosemeyer, H.; Herdewijn, P.; Lescrinier, E.

Citation:

Citation: Mattelaer, C.; Maiti, M.; Smets, L.; Maiti, M.; Schepers, G.; Mattelaer, H.; Rosemeyer, H.; Herdewijn, P.; Lescrinier, E.. "Stable hairpin structures formed by xylose based nucleic acids." Chembiochem 22, 1638-1645 (2021).
PubMed: 33427360

Assembly members:

Assembly members:
entity_1, polymer, 20 residues, 6062.983 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AGCAATCCXXXXGGATTGCT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	85
1H chemical shifts	167

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 20 residues - 6062.983 Da.

1		DA	DG	DC	DA	DA	DT	DC	DC	XC	XC
2		XC	XC	DG	DG	DA	DT	DT	DG	DC	DT

Samples:

sample_1: oligomer 2.9 mM

sample_conditions_1: ionic strength: 0 M; pH: 6.6 pD; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	anisotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

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

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE II 600 MHz