BMRB Entry 17887
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17887
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: DNA sequence context conceals alpha anomeric lesion PubMed: 22227386
Deposition date: 2011-08-27 Original release date: 2012-01-18
Authors: Johnson, Christopher; Spring, Alexander; Cunningham, Richard; Germann, Markus
Citation: Johnson, Christopher; Spring, Alexander; Desai, Sunil; Cunningham, Richard; Germann, Markus. "DNA Sequence Context Conceals -Anomeric Lesions." J. Mol. Biol. 416, 425-437 (2012).
Assembly members:
DNA_(5'-D(*GP*TP*CP*CP*ADA*GP*GP*AP*CP*G)-3')_, polymer, 10 residues, 2756.833 Da.
DNA_(5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')_, polymer, 10 residues, 3021.004 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 Host organism: n/a
Entity Sequences (FASTA):
DNA_(5'-D(*GP*TP*CP*CP*ADA*GP*GP*AP*CP*G)-3')_: GTCCXGGACG
DNA_(5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')_: CGTCCTGGAC
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 56 |
| 1H chemical shifts | 171 |
| 31P chemical shifts | 18 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA_chain_1 | 1 |
| 2 | DNA_chain_2 | 2 |
Entities:
Entity 1, DNA_chain_1 10 residues - 2756.833 Da.
| 1 | DG | DT | DC | DC | A3A | DG | DG | DA | DC | DG |
Entity 2, DNA_chain_2 10 residues - 3021.004 Da.
| 1 | DC | DG | DT | DC | DC | DT | DG | DG | DA | DC |
Samples:
water_sample: DNA_chain_1 0.75 mM; DNA_chain_2 0.75 mM; sodium phosphate 10 mM; sodium chloride 50 mM; D2O 10%; DSS 0.2 uM; EDTA 2 mM; H2O 90%
D2O_sample: DNA_chain_1 0.75 mM; DNA_chain_2 0.75 mM; sodium phosphate 10 mM; sodium chloride 50 mM; D2O 100%; DSS 0.2 uM; EDTA 2 mM
sample_conditions_1: ionic strength: 50 mM; pH: 6.65; pressure: 1 atm; temperature: 276 K
sample_conditions_2: ionic strength: 50 mM; pH*: 7.05; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 1-1 jump return | water_sample | isotropic | sample_conditions_1 |
| 1D NOE | water_sample | isotropic | sample_conditions_1 |
| 1-1 NOESY 2D 150 ms | water_sample | isotropic | sample_conditions_1 |
| Low Flip COSY | D2O_sample | isotropic | sample_conditions_2 |
| TOCYS | D2O_sample | isotropic | sample_conditions_2 |
| 2D 1H 1H NOESY 75 ms | D2O_sample | isotropic | sample_conditions_2 |
| 2D 1H 1H NOESY 125 ms | D2O_sample | isotropic | sample_conditions_2 |
| 2D 1H-1H NOESY 250 ms | D2O_sample | isotropic | sample_conditions_2 |
| Constant Time COSY | D2O_sample | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC | D2O_sample | isotropic | sample_conditions_2 |
| 2D 1H-31P CORR | D2O_sample | isotropic | sample_conditions_2 |
| 1D 31P | D2O_sample | isotropic | sample_conditions_2 |
Software:
AMBER v9.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - structure solution
SPARKY v3.3, Goddard - chemical shift assignment
TOPSPIN, Bruker Biospin - data analysis
CORMA, Thomas James - structure solution
MARDGIRAS, Thomas James - structure solution
CURVES v5.1, Heinz Sklenar, Richard Lavery - analysis
NMR spectrometers:
- Bruker Avance 600 MHz