BMRB Entry 34591

Name: GA attached to an i-motif clip at 3'-end
Published: 2021-11-05

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PDB ID: 7bl0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34591
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:

GA attached to an i-motif clip at 3'-end

Deposition date:

2021-01-17

Original release date:

2021-11-05

Authors:

Novotny, A.; Novotny, J.

Citation:

Citation: Novotny, A.; Novotny, J.; Kejnovka, I.; Vorlickova, M.; Fiala, R.; Marek, R.. "Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip" Nucleic Acids Res. 49, 11425-11437 (2021).
PubMed: 34718718

Assembly members:

Assembly members:
entity_1, polymer, 5 residues, 1481.044 Da.
entity_2, polymer, 5 residues, 1480.036 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAXCX
entity_2: GACXX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	43

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1
3	unit_3	2
4	unit_4	2

Entities:

Entity 1, unit_1 5 residues - 1481.044 Da.

1

DG

DA

DNR

DC

U48

Entity 2, unit_3 5 residues - 1480.036 Da.

1

DG

DA

DC

DNR

5CM

Samples:

sample_1: GAGACC(5MeC), entity_1 0.8 ± 0.1 mM; GAGACC(5MeC), entity_2 0.8 ± 0.1 mM

sample_2: GAGACC(5MeC), entity_1 0.8 ± 0.1 mM; GAGACC(5MeC), entity_2 0.8 ± 0.1 mM

sample_conditions_1: ionic strength: 60 mM; pH: 5; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 60 mM; pH: 5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

NMRFAM-SPARKY v1.413, National Magnetic Resonance Facility at Madison - chemical shift assignment

TopSpin v4, Bruker Biospin - collection

Amber v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE III HD 700 MHz