BMRB Entry 25882
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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/BMR25882
MolProbity Validation Chart
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NMR-STAR v3 text file.
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Citation: Woo, Christina; Li, Zhenwu; Paulson, Eric; Herzon, Seth. "Structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A" Proc. Natl. Acad. Sci. U.S.A. 113, 2851-2856 (2016).
PubMed: 26929332
Assembly members:
DNA_(5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3'), polymer, 8 residues, Formula weight is not available
(1R,1'R,2S,2'S,3R,3'R,5a'R,10a'R,11aS)-2'-[(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)oxy]-2,2'-diethyl-11,11'-dihydrazinyl-6,6',9,9'-tetrahydroxy-4,4',5,5',10,10'-hexaoxo-1,1'-bis{[2,4,6-trideoxy-4-(dimethylamino)-beta-L-arabino-hexopyranosyl]oxy}-2,2',3,3',4,4',5,5',5a',8',10,10',10a',11a-tetradecahydro-1H,1'H-3,3'-bibenzo[b]fluoren-2-yl 2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranoside, non-polymer, 1375.468 Da.
Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
DNA_(5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3'): GCTATAGC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 234 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3') | 1 |
| 2 | DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3') | 1 |
| 3 | lomaiviticin A | 2 |
Entities:
Entity 1, DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP)-3') 8 residues - Formula weight is not available
| 1 | DG | DC | DT | DA | DT | DA | DG | DC |
Entity 2, lomaiviticin A - C68 H90 N6 O24 - 1375.468 Da.
| 1 | 4JF |
Samples:
sample_1: DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP))-3') 2.2 uM; lomaiviticin A 1.1 uM; sodium phospate 10 mM; sodium chloride 25 mM; D2O, [U-2H], 100%
sample_2: DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*CP))-3') 2.2 uM; lomaiviticin A 1.1 uM; sodium phospate 10 mM; sodium chloride 25 mM; H2O 90%; D2O, [U-2H], 10%
sample_conditions_1: ionic strength: 24 mM; pH: 7.5; pressure: 1 atm; temperature: 297 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_2 | isotropic | sample_conditions_1 |
Software:
AMBER v14, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution
NMR spectrometers:
- Agilent DD2 800 MHz