BMRB Entry 18835
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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/BMR18835
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Title: Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex PubMed: 23748954
Deposition date: 2012-11-09 Original release date: 2013-06-10
Authors: Kowal, Ewa; Lad, Rahul; Pallan, Pradeep; Muffly, Elizabeth; Wawrzak, Zdzislaw; Egli, Martin; Sturla, Shana; Stone, Michael
Citation: Kowal, Ewa; Lad, Rahul; Pallan, Pradeep; Dhummakupt, Elizabeth; Wawrzak, Zdzislaw; Egli, Martin; Sturla, Shana; Stone, Michael. "Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction." Nucleic Acids Res. 41, 7566-7576 (2013).
Assembly members:
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', polymer, 12 residues, 2755.845 Da.
Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3': CGCGAATTXGCG
- assigned_chemical_shifts
- homonucl_NOEs
| Data type | Count |
| 1H chemical shifts | 107 |
| homonuclear NOE values | 153 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | strand 1 | 1 |
| 2 | strand 2 | 1 |
Entities:
Entity 1, strand 1 12 residues - 2755.845 Da.
| 1 | DC | DG | DC | DG | DA | DA | DT | DT | D3N | DG | ||||
| 2 | DC | DG |
Samples:
sample_1: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3' 0.53 mM; D2O, [U-100% 2H], 100%; sodium chloride 100 mM; EDTA 50 uM; sodium phosphate 10 mM
sample_2: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3' 0.53 mM; D2O, [U-100% 2H], 90%; H2O 10%; sodium phosphate 10 mM; EDTA 50 uM; sodium chloride 100 mM
sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 283 K
sample_conditions_2: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 278 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
TOPSPIN, Bruker Biospin - collection, processing
CORMA, Thomas L. James - data analysis
CURVES v5.3, Ravishankar, G. et al. - data analysis
MARDIGRAS, Thomas L. James - processing
SPARKY, Goddard - chemical shift assignment, chemical shift calculation
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz