BMRB Entry 34296
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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/BMR34296
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Title: Polyamide - DNA complex NMR structure PubMed: 30407668
Deposition date: 2018-07-03 Original release date: 2018-11-21
Authors: Aman, K.
Citation: Aman, Khalid; Padroni, Giacomo; Parkinson, John; Welte, Thomas; Burley, Glenn. "Structural and Kinetic Profiling of Allosteric Modulation of Duplex DNA Induced by DNA-Binding Polyamide Analogues." Chemistry 25, 2757-2763 (2019).
Assembly members:
entity_1, polymer, 13 residues, 3940.603 Da.
entity_FGW, non-polymer, 1250.372 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: XCGATGTACATCG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 250 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1, 1 | 1 |
| 2 | entity_1, 2 | 1 |
| 3 | entity_2 | 2 |
Entities:
Entity 1, entity_1, 1 13 residues - 3940.603 Da.
| 1 | PA9 | DC | DG | DA | DT | DG | DT | DA | DC | DA | ||||
| 2 | DT | DC | DG |
Entity 2, entity_2 - C60 H75 N21 O10 - 1250.372 Da.
| 1 | FGW |
Samples:
sample_1: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3') 1.26 mM; polyamide (PA9) 0.24 mM
sample_2: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3') 1.26 mM; polyamide (PA9) 0.24 mM
sample_conditions_1: pH: 7.4; 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 COSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
TOPSPIN, Bruker Biospin - collection
AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation
SPARKY, Goddard - chemical shift assignment, peak picking
NMR spectrometers:
- Bruker AvanceII 600.13 MHz