BMRB Entry 16225
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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/BMR16225
MolProbity Validation Chart
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NMR-STAR v3 text file.
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RDF gzip file.
All files associated with the entry
Citation: Brown, Kyle; Roginskaya, Marina; Zou, Yue; Altamirano, Alvin; Basu, Ashis; Stone, Michael. "Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site" Nucleic Acids Res. 38, 428-440 (2010).
PubMed: 19892827
Assembly members:
DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3'), polymer, 12 residues, 3392.232 Da.
DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3'), polymer, 12 residues, 3609.425 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(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3'): GTGCGXGTTTGT
DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3'): ACAAACACGCAC
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 231 |
| 31P chemical shifts | 20 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DNA (5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3') | 1 |
| 2 | DNA (5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3') | 2 |
Entities:
Entity 1, DNA (5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3') 12 residues - 3392.232 Da.
| 1 | DG | DT | DG | DC | DG | CTG | DG | DT | DT | DT | ||||
| 2 | DG | DT |
Entity 2, DNA (5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3') 12 residues - 3609.425 Da.
| 1 | DA | DC | DA | DA | DA | DC | DA | DC | DG | DC | ||||
| 2 | DA | DC |
Samples:
sample_1: DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3') 1 mM; DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3') 1 mM; sodium phosphate 20 mM; sodium chloride 100 mM; sodium azide 10 uM; EDTA 50 uM
sample_2: DNA_(5'-D(*DGP*DTP*DGP*DCP*DGP*(TG)P*DGP*DTP*DTP*DTP*DGP*DT)-3') 1 mM; DNA_(5'-D(*DAP*DCP*DAP*DAP*DAP*DCP*DAP*DCP*DGP*DCP*DAP*DC)-3') 1 mM; sodium phosphate 20 mM; sodium chloride 100 mM; sodium azide 10 uM; EDTA 50 uM
sample_conditions_1: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 303 K
sample_conditions_2: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 278 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D 31P-1H COSY | sample_1 | isotropic | sample_conditions_1 |
Software:
AMBER v9, Delaglio, Zhengrong and Bax - refinement
SPARKY, Goddard - chemical shift assignment, data analysis
TOPSPIN, Bruker Biospin - processing
MARDIGRAS, Borgias, B.A. & James, T.L. - restraint generation
CORMA, James T.L. - structure validation
CURVES, Lavery, R. and Sklenar, H - data analysis, structure analysis
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz