BMRB Entry 34386

Name: SC14 G-hairpin
Published: 2021-02-01

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PDB ID: 6r8e
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34386
MolProbity Validation Chart

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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:

SC14 G-hairpin

Deposition date:

2019-04-01

Original release date:

2021-02-01

Authors:

Lenarcic Zivkovic, M.; Trantirek, L.; Plavec, J.

Citation:

Citation: Zdivkovic, Martina Lenarcic; Gajarsky, Martin; Bekova, Katerina; Stadlbauer, Petr; Vicherek, Lukas; Petrova, Magdalena; Fiala, Radovan; Rosenberg, Ivan; Sponer, Jiri; Plavec, Janez; Trantirek, Lukas. "Insight into formation propensity of pseudocircular DNA G-hairpins" Nucleic Acids Res. 49, 2317-2332 (2021).
PubMed: 33524154

Assembly members:

Assembly members:
entity_1, polymer, 14 residues, 4413.846 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GTGTGTGGGTGTGT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	135

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 14 residues - 4413.846 Da.

1

DG

DT

DG

DT

DG

DT

DG

DT

2

DG

DT

DG

DT

Samples:

sample_1: DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3') 0.6 mM

sample_2: DNA (5'-D(*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*GP*T)-3') 0.6 mM

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 120 mM; pH: 7.0 pD; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_2
2D TOCSY	sample_2	isotropic	sample_conditions_2
2D DQF COSY	sample_2	isotropic	sample_conditions_2
1D 15N-edited HSQC	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment

AMBER14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

VNMR, Varian - processing

TOPSPIN, Bruker Biospin - processing

NMR spectrometers:

Bruker AvanceIII 700 MHz
Bruker AvanceIII 850 MHz
Agilent DD2 600 MHz
Bruker AvanceIII 950 MHz
Bruker AvanceIII 600 MHz