BMRB Entry 30052

Name: NMR solution structure of [Rp, Rp]-PT dsDNA
Published: 2016-11-14

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PDB ID: 5j3f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30052
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of [Rp, Rp]-PT dsDNA

Deposition date:

2016-03-30

Original release date:

2016-11-14

Authors:

Lan, Wenxian; Hu, Zhongpei; Cao, Chunyang

Citation:

Citation: Lan, Wenxian; Hu, Zhongpei; Cao, Chunyang. "Structural investigation into physiological DNA phosphorothioate modification" Sci. Rep. 6, 25737-25737 (2016).
PubMed: 27169778

Assembly members:

Assembly members:
DNA (5'-D(*CP*GP*(RSG)P*CP*CP*GP*CP*CP*GP*A)-3'), polymer, 10 residues, 3047.047 Da.
DNA (5'-D(*TP*CP*GP*GP*CP*GP*(RSG)P*CP*CP*G)-3'), polymer, 10 residues, 3078.058 Da.

Natural source:

Natural source: Common Name: high GC Gram+ Taxonomy ID: 1916 Superkingdom: Bacteria Kingdom: not available Genus/species: Streptomyces lividans

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Streptomyces lividans

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*(RSG)P*CP*CP*GP*CP*CP*GP*A)-3'): CGXCCGCCGA
DNA (5'-D(*TP*CP*GP*GP*CP*GP*(RSG)P*CP*CP*G)-3'): TCGGCGXCCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
1H chemical shifts	144
31P chemical shifts	18

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 10 residues - 3047.047 Da.

1

DC

DG

GS

DC

DG

DC

DG

DA

Entity 2, entity_2 10 residues - 3078.058 Da.

1

DT

DC

DG

DC

DG

GS

DC

DG

Samples:

sample_1: [Rp, Rp]-PT dsDNA 1.0 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 360 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K

sample_conditions_2: ionic strength: 360 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	anisotropic	sample_conditions_1
2D TOCSY	sample_1	anisotropic	sample_conditions_2
2D DQF-COSY	sample_1	anisotropic	sample_conditions_2
2D NOESY	sample_1	anisotropic	sample_conditions_2
2D 1H-31P hetcor	sample_1	anisotropic	sample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Agilent DD2 600 MHz
Agilent DD2 500 MHz