BMRB Entry 30253
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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/BMR30253
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Title: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A2-DNA structure PubMed: 28369571
Deposition date: 2017-02-26 Original release date: 2017-04-03
Authors: Sathyamoorthy, B.; Shi, H.; Xue, Y.; Al-Hashimi, H.
Citation: Sathyamoorthy, B.; Shi, H.; Zhou, H.; Xue, Y.; Rangadurai, A.; Merriman, D.; Al-Hashimi, H.. "Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A" Nucleic Acids Res. 45, 5586-5601 (2017).
Assembly members:
entity_1, polymer, 12 residues, 3678.403 Da.
entity_2, polymer, 12 residues, 3647.393 Da.
Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: GCATCGATTGGC
entity_2: GCCAATCGATGC
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 113 |
| 15N chemical shifts | 10 |
| 1H chemical shifts | 155 |
| 31P chemical shifts | 22 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 12 residues - 3678.403 Da.
| 1 | DG | DC | DA | DT | DC | DG | DA | DT | DT | DG | ||||
| 2 | DG | DC |
Entity 2, entity_2 12 residues - 3647.393 Da.
| 1 | DG | DC | DC | DA | DA | DT | DC | DG | DA | DT | ||||
| 2 | DG | DC |
Samples:
sample_1: DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') 3.25 ± 0.25 mM; DNA (5'-D(*GP*CP*CP*AP*AP*TP*CP*GP*AP*TP*GP*C)-3') 3.25 ± 0.25 mM; sodium phosphate buffer 15 mM; sodium chloride 25 mM; EDTA 0.1 mM
sample_2: DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') 3.25 ± 0.25 mM; DNA (5'-D(*GP*CP*CP*AP*AP*TP*CP*GP*AP*TP*GP*C)-3') 3.25 ± 0.25 mM; sodium phosphate buffer 15 mM; sodium chloride 25 mM; EDTA 0.1 mM
sample_conditions_1: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N SOFAST-HMQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C SOFAST-HMQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-31P HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C TROSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C TROSY | sample_2 | anisotropic | sample_conditions_2 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY vNMRFAM, Goddard - chemical shift assignment, peak picking
TOPSPIN, Bruker Biospin - collection
VNMR, Varian - collection
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation
NMR spectrometers:
- Varian INOVA 800 MHz
- Bruker AvanceII 600 MHz