BMRB Entry 30105

Name: Structural impact of single ribonucleotides in DNA
Published: 2016-08-22

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PDB ID: 5kgv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30105
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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:

Structural impact of single ribonucleotides in DNA

Deposition date:

2016-06-13

Original release date:

2016-08-22

Authors:

Evich, M.; Spring-Connell, A.; Storici, F.

Citation:

Citation: Evich, M.; Spring-Connell, A.; Storici, F.; Germann, M.. "Structural impact of single ribonucleotides in DNA." Chembiochem 17, 1968-1977 (2016).
PubMed: 27504600

Assembly members:

Assembly members:
entity_1, polymer, 9 residues, 2771.823 Da.
entity_2, polymer, 9 residues, 2715.799 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 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):
entity_1: ATGGAGCTC
entity_2: GAGCTCCAT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	128
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	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 9 residues - 2771.823 Da.

1

DA

DT

DG

DA

G

DC

DT

DC

Entity 2, entity_2 9 residues - 2715.799 Da.

1

DG

DA

DG

DC

DT

DC

DA

DT

Samples:

sample_1: D2O, 100% deuterium, 100%; DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 1 mM; DNA/RNA (5'-D(*AP*TP*GP*GP*A)-R(P*G)-D(P*CP*TP*C)-3') 1 mM; sodium chloride 100 mM; sodium phosphate 10 mM

sample_2: D2O, 100% deuterium, 10%; DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 1 mM; DNA/RNA (5'-D(*AP*TP*GP*GP*A)-R(P*G)-D(P*CP*TP*C)-3') 1 mM; sodium chloride 100 mM; sodium phosphate 10 mM

sample_conditions_1: ionic strength: 0.1 mM; pH: 6.6; pressure: 1 atm; temperature: 294 K

sample_conditions_2: ionic strength: 0.1 mM; pH: 7.0; pressure: 1 atm; temperature: 294 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY 250 ms	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_2
2D Low Flip COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	anisotropic	sample_conditions_1
2D constant time NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-31P CORR	sample_1	isotropic	sample_conditions_1
2D NOESY 150 ms	sample_1	isotropic	sample_conditions_1
1D 1H	sample_1	isotropic	sample_conditions_1
1D 31P	sample_1	isotropic	sample_conditions_1
1D 1H 1-1 jump and return	sample_2	isotropic	sample_conditions_2

Software:

AMBER v9, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

CORMA, Thomas James - refinement

MARDIGRAS, Thomas James - refinement

SPARKY v3.33, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 600 MHz
Bruker AvanceIII 850 MHz