BMRB Entry 34579
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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/BMR34579
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
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Citation: Lomzov, A.; Sviridov, E.; Shernuykov, A.; Shevelev, G.; Pyshnyi, D.; Bagryanskaya, E.. "Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels." J. Phys. Chem. B 120, 5125-5133 (2016).
PubMed: 27195671
Assembly members:
entity_1, polymer, 10 residues, 3005.969 Da.
entity_2, polymer, 10 residues, 3086.016 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: CACGCCGCTG
entity_2: CAGCGGCGTG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 265 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
Entities:
Entity 1, unit_1 10 residues - 3005.969 Da.
| 1 | DC | DA | DC | DG | DC | DC | DG | DC | DT | DG |
Entity 2, unit_2 10 residues - 3086.016 Da.
| 1 | DC | DA | DG | DC | DG | DG | DC | DG | DT | DG |
Samples:
sample_1: DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3') 1.1 ± 0.05 mM; DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3') 1.1 ± 0.05 mM; sodium phosphate 10 ± 0.5 mM; sodium chloride 100 ± 5 mM; EDTA 200 ± 10 mM
sample_2: DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3') 1.1 ± 0.05 mM; DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3') 1.1 ± 0.05 mM; sodium phosphate 10 ± 0.5 mM; sodium chloride 100 ± 5 mM; EDTA 200 ± 10 mM
sample_conditions_1: ionic strength: 510 mM; pH: 7.2; pressure: 1 atm; temperature: 288.4 K
sample_conditions_2: ionic strength: 510 mM; pH: 7.2; pressure: 1 atm; temperature: 306.5 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_2 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_2 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
Amber v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation
CcpNmr Analysis v2.3.1, CcpNmr - chemical shift assignment, peak picking
NMR spectrometers:
- Bruker AVIII 600 MHz