BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 17535

Title: DNA / RNA Hybrid containing a central stereo specific Rp borano phosphate linkage   PubMed: 21443203

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

Data sets:
Data typeCount
11B chemical shifts1
13C chemical shifts36
1H chemical shifts130
31P chemical shifts16

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA_chain_A1
2RNA_chain_B2

Entities:

Entity 1, DNA_chain_A 9 residues - 2417.623 Da.

1   DADTDGDGDTBGRDCDTDC

Entity 2, RNA_chain_B 9 residues - 2854.802 Da.

1   GAGCACCAU

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYH2O_D2Oisotropicsample_conditions_1
2D 1H-13C HSQCD2Oisotropicsample_conditions_1
2D 1H-1H TOCSYD2Oisotropicsample_conditions_1
2D DQF-COSYD2Oisotropicsample_conditions_1
2D 1H-1H NOESYD2Oisotropicsample_conditions_1
2D 1H-31P CORRD2Oisotropicsample_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

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