BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 34378

Title: Structure of kiteplatinated dsDNA

Deposition date: 2019-03-13 Original release date: 2020-03-27

Authors: Margiotta, N.; Papadia, P.; Kubicek, K.; Krejcikova, M.; Gkionis, K.; Sponer, J.

Citation: Krejcikova, M.; Papadia, P.; Gkionis, K.; Plats, J.; Petruzzella, E.; Savino, S.; Hoeschelle, J.; Natile, G.; Sponer, J.; Kubicek, K.; Margiotta, N.. "Structural characterization of kiteplatinated DNA"  . ., .-..

Assembly members:
entity_1, polymer, 12 residues, 3559.319 Da.
entity_2, polymer, 12 residues, 3768.453 Da.
entity_LN8, non-polymer, 380.173 Da.

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: CCTCAGGCCTCC
entity_2: GGAGGCCTGAGG

Data sets:
Data typeCount
1H chemical shifts200

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_33

Entities:

Entity 1, entity_1 12 residues - 3559.319 Da.

1   DCDCDTDCDADGDGDCDCDT
2   DCDC

Entity 2, entity_2 12 residues - 3768.453 Da.

1   DGDGDADGDGDCDCDTDGDA
2   DGDG

Entity 3, entity_3 - C6 H14 Cl2 N2 Pt - 380.173 Da.

1   LN8

Samples:

sample_1: entity_1 1 mM; entity_2 1 mM; kiteplatin 1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_2
2D 1H-15N HSQCsample_1isotropicsample_conditions_2
2D 1H-1H TOCSYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

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

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 850 MHz
  • Bruker AVANCE III 950 MHz