BMRB Entry 17535

Name: DNA / RNA Hybrid containing a central stereo specific Rp borano phosphate linkage
Published: 2011-05-12

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PDB ID: 2lar
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17535
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

DNA / RNA Hybrid containing a central stereo specific Rp borano phosphate linkage

Deposition date:

2011-03-18

Original release date:

2011-05-12

Authors:

Johnson, Christopher; Spring, Alexander; Shaw, Barbara; Germann, Markus

Citation:

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).
PubMed: 21443203

Assembly members:

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:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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:

assigned_chemical_shifts
- Assigned_chem_shifts

Data type	Count
11B chemical shifts	1
13C chemical shifts	36
1H chemical shifts	130
31P chemical shifts	16

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

DT

BGR

DC

DT

DC

Entity 2, RNA_chain_B 9 residues - 2854.802 Da.

1

G

A

G

C

A

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