BMRB Entry 11528
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11528
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: STRUCTURE OF METALLO-DNA IN SOLUTION
Deposition date: 2013-06-17 Original release date: 2014-03-03
Authors: Yamaguchi, H.; Sebera, J.; Kondo, J.; Oda, S.; Komuro, T.; Kawamura, T.; Dairaku, T.; Kondo, Y.; Okamoto, I.; Ono, A.; Burda, J.; Kojima, C.; Sychrovsky, V.; Tanaka, Y.
Citation: Yamaguchi, H.; Sebera, J.; Kondo, J.; Oda, S.; Komuro, T.; Kawamura, T.; Dairaku, T.; Kondo, Y.; Okamoto, I.; Ono, A.; Burda, J.; Kojima, C.; Sychrovsky, V.; Tanaka, Y.. "The structure of metallo-DNA with consecutive T-Hg(II)-T base-pairs explains positive entropy for the metallo-base-pair formation" .
Assembly members:
5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3', polymer, 10 residues, 3011.991 Da.
5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3', polymer, 10 residues, 3061.029 Da.
MERCURY (II) ION, non-polymer, 200.590 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 Host organism: not applicable Vector: not applicable
Entity Sequences (FASTA):
5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3': CGCGTTGTCC
5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3': GGACTTCGCG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 220 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' | 1 |
| 2 | 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' | 2 |
| 3 | MERCURY (II) ION_1 | 3 |
| 4 | MERCURY (II) ION_2 | 3 |
Entities:
Entity 1, 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 10 residues - 3011.991 Da.
| 1 | DC | DG | DC | DG | DT | DT | DG | DT | DC | DC |
Entity 2, 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 10 residues - 3061.029 Da.
| 1 | DG | DG | DA | DC | DT | DT | DC | DG | DC | DG |
Entity 3, MERCURY (II) ION_1 - Hg - 200.590 Da.
| 1 | HG |
Samples:
sample_1: 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 2.0 mM; 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 2.0 mM; Mercury(II) perchlorate 4.0 mM; Sodium perchlorate 100 mM; D2O, [U-100% 2H], 100%
sample_2: 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3' 2.0 mM; 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3' 2.0 mM; Mercury(II) perchlorate 4.0 mM; Sodium perchlorate 100 mM; H2O 95%; D2O, [U-100% 2H], 5%
sample_conditions_1: ionic strength: 0.10 M; pH: 6.0; pressure: 1 atm; temperature: 293 K
sample_conditions_2: ionic strength: 0.10 M; pH: 6.0; pressure: 1 atm; temperature: 283 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
Software:
X-PLOR v3.851, A. T. BRUNGER - refinement, structure solution
SPARKY v3.1, Goddard - chemical shift assignment, peak picking, processing
MARDIGRAS, Thomas L. James - structure solution
NMR spectrometers:
- BRUKER DRX800 800 MHz