BMRB Entry 30191
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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/BMR30191
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Title: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd Position and 9th position
Deposition date: 2016-10-12 Original release date: 2018-04-27
Authors: Hoppins, J.; Miears, H.; Gruber, D.; Kasymov, R.; Zharkov, D.; Smirnov, S.
Citation: Hoppins, J.; Miears, H.; Gruber, D.; Kasymov, R.; Zharkov, D.; Smirnov, S.. "Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd Position and 9th position" . ., .-..
Assembly members:
entity_1, polymer, 12 residues, 3691.446 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: CGXGAATTXGCG
- assigned_chemical_shifts
Data type | Count |
1H chemical shifts | 190 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | entity_1, 1 | 1 |
2 | entity_1, 2 | 1 |
Entities:
Entity 1, entity_1, 1 12 residues - 3691.446 Da.
1 | DC | DG | 5CM | DG | DA | DA | DT | DT | 5CM | DG | ||||
2 | DC | DG |
Samples:
sample_1: DNA (5'-D(*CP*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3') 1 mM; EDTA 0.1 mM; potassium phosphate 10 mM; sodium chloride 50 mM
sample_conditions_1: ionic strength: 120 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
sample_conditions_2: ionic strength: 120 mM; pH: 6.8; 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 NOESY | sample_1 | isotropic | sample_conditions_2 |
2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
Software:
AMBER v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView v9.0, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking
NMR spectrometers:
- Varian INOVA 500 MHz