BMRB Entry 17535
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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/BMR17535
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Title: DNA / RNA Hybrid containing a central stereo specific Rp borano phosphate linkage PubMed: 21443203
Deposition date: 2011-03-18 Original release date: 2011-05-12
Authors: Johnson, Christopher; Spring, Alexander; Shaw, Barbara; Germann, Markus
Citation: Johnson, Christopher; Spring, Alexander; Sergueev, Dimitri; Shaw, Barbara; Germann, Markus. "Structural Basis of the RNase H1 Activity on Stereo Regular Borano Phosphonate DNA/RNA Hybrids." Biochemistry 50, 3903-3912 (2011).
Assembly members:
DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_, polymer, 9 residues, 2417.623 Da.
RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_, polymer, 9 residues, 2854.802 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):
DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_: ATGGTXCTC
RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_: GAGCACCAU
- assigned_chemical_shifts
| Data type | Count |
| 11B chemical shifts | 1 |
| 13C chemical shifts | 36 |
| 1H chemical shifts | 130 |
| 31P chemical shifts | 16 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA_chain_A | 1 |
| 2 | RNA_chain_B | 2 |
Entities:
Entity 1, DNA_chain_A 9 residues - 2417.623 Da.
| 1 | DA | DT | DG | DG | DT | BGR | DC | DT | DC |
Entity 2, RNA_chain_B 9 residues - 2854.802 Da.
| 1 | G | A | G | C | A | C | C | A | U |
Samples:
H2O_D2O: DNA_chain_A 1.0 mM; RNA_chain_B 1.0 mM; sodium chloride 50 mM; sodium phosphate 10 mM; EDTA 0.5 mM; DSS 0.3 uM; D2O 10%; H2O 90%
D2O: DNA_chain_A 1.0 mM; RNA_chain_B 1.0 mM; sodium chloride 50 mM; sodium phosphate 10 mM; EDTA 0.5 mM; DSS 0.3 uM; D2O 99.999%
sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | H2O_D2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | D2O | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | D2O | isotropic | sample_conditions_1 |
| 2D DQF-COSY | D2O | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | D2O | isotropic | sample_conditions_1 |
| 2D 1H-31P CORR | D2O | isotropic | sample_conditions_1 |
Software:
AMBER v9.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - geometry optimization, refinement, structure solution
xwinnmr v3.5, Bruker Biospin - collection
TOPSPIN v2.1, Bruker Biospin - chemical shift calculation, data analysis, processing
CORMA v5.21, (CORMA) Dr. Thomas James - data analysis
MARDIGRAS v5.21, Thomas James - refinement
SPARKY v3.98, Goddard - chemical shift assignment, data analysis
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 500 MHz