BMRB Entry 30113

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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/BMR30113
MolProbity Validation Chart

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Title:
Structural impact of single ribonucleotides in DNA
Deposition date:
2016-06-16
Original release date:
2016-08-22
Authors:
Evich, M.; Spring-Connell, A.; Storici, F.; Germann, M.
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: ATCCGGTAG
entity_2: CTACCGGAT

Data sets:
Data typeCount
1H chemical shifts128
31P chemical shifts16

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 9 residues - 2771.823 Da.

1   DADTDCDCGDGDTDADG

Entity 2, entity_2 9 residues - 2715.799 Da.

1   DCDTDADCDCDGDGDADT

Samples:

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

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

sample_conditions_1: ionic strength: 110 mM; pH: 6.6 pH*; pressure: 1 atm; temperature: 294 K

sample_conditions_2: ionic strength: 110 mM; pH: 7.0; pressure: 1 atm; temperature: 294 K

Experiments:

NameSampleSample stateSample conditions
2D NOESY 250 mssample_1isotropicsample_conditions_1
2D NOESYsample_2isotropicsample_conditions_2
2D Low Flip COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-31P CORRsample_1isotropicsample_conditions_1
2D constant time NOESYsample_1isotropicsample_conditions_1
2D NOESY 150 mssample_1isotropicsample_conditions_1
1D 1Hsample_1isotropicsample_conditions_1
1D 1H 1-1 jump and returnsample_2isotropicsample_conditions_2
1D 31Psample_1isotropicsample_conditions_1

Software:

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

CORMA, Thomas James - refinement

MARDIGRAS, Thomas James - processing

SPARKY v3.33, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker AvanceIII 850 MHz