BMRB Entry 34592
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34592
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Title: AG repetition attached to a compact i-motif clip at 3'-end PubMed: 34718718
Deposition date: 2021-01-18 Original release date: 2021-11-05
Authors: Novotny, A.; Novotny, J.
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).
Assembly members:
entity_1, polymer, 7 residues, 2109.429 Da.
entity_2, polymer, 7 residues, 2108.421 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: AGAGXCX
entity_2: AGAGCXC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 50 |
Additional metadata:
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 7 residues - 2109.429 Da.
| 1 | DA | DG | DA | DG | DNR | DC | DNR |
Entity 2, unit_3 7 residues - 2108.421 Da.
| 1 | DA | DG | DA | DG | DC | DNR | DC |
Samples:
sample_1: AGAGCCC, entity_1 1.3 ± 0.1 mM; AGAGCCC, entity_2 1.3 ± 0.1 mM
sample_2: AGAGCCC, entity_1 1.3 ± 0.1 mM; AGAGCCC, entity_2 1.3 ± 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: 288 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:
Amber v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation
NMRFAM-SPARKY v1.413, Nuclear Magnetic Resonance Facility at Madison - chemical shift assignment
TopSpin v4, Bruker Biospin - collection
NMR spectrometers:
- Bruker AVANCE III HD 700 MHz