BMRB Entry 34157

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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/BMR34157
MolProbity Validation Chart

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Title:
NtMe polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies
Deposition date:
2017-07-05
Original release date:
2017-12-14
Authors:
Padroni, G.; Parkinson, J.; Burley, G.
Citation:

Citation: Padroni, Giacomo; Parkinson, John; Fox, Keith; Burley, Glenn. "Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides."  Nucleic Acids Res. 46, 42-53 (2017).
PubMed: 29194552

Assembly members:

Assembly members:
DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), polymer, 12 residues, 3582.424 Da.
5-methyl-1,3-thiazole-4-carboxylic acid, non-polymer, 143.164 Da.
4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID, non-polymer, 140.140 Da.
GAMMA-AMINO-BUTANOIC ACID, non-polymer, 103.120 Da.
4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID, non-polymer, 141.128 Da.
3-(3-azaniumylpropanoylamino)propyl-dimethyl-azanium, non-polymer, 175.272 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'): XGATGTACATCG

Data sets:
Data typeCount
13C chemical shifts131
1H chemical shifts428
31P chemical shifts22

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_2, 12
4entity_3, 13
5entity_3, 23
6entity_3, 33
7entity_4, 14
8entity_5, 15
9entity_3, 43
10entity_3, 53
11entity_3, 63
12entity_6, 16

Entities:

Entity 1, entity_1, 1 12 residues - 3582.424 Da.

1   DCZDGDADTDGDTDADCDADT
2   DCDG

Entity 2, entity_2, 1 - C5 H5 N O2 S - 143.164 Da.

1   9T5

Entity 3, entity_3, 1 - C6 H8 N2 O2 - 140.140 Da.

1   PYB

Entity 4, entity_4, 1 - C4 H9 N O2 - 103.120 Da.

1   ABU

Entity 5, entity_5, 1 - C5 H7 N3 O2 - 141.128 Da.

1   IMT

Entity 6, entity_6, 1 - C8 H21 N3 O - 175.272 Da.

1   9T8

Samples:

sample_1: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3') 1.3 nM; PA6 1.3 mM; Phosphate 100 mM

sample_2: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3') 1.3 mM; PA6 1.3 mM; Phosphate 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
1H-31P COSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment

MARDIGRAS, N. Ulyanov - geometry optimization

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

NMR spectrometers:

  • Bruker Avance 600 MHz