1MP7
A Third Complex of Post-Activated Neocarzinostatin Chromophore with DNA. Bulge DNA Binding from the Minor Groove
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 0.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.0 | 90% H2O-10% D2O, 100% D2O | 10 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0 | 6.0 | ambient | 268 | |
2 | 2D TOCSY | 0.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.0 | 90% H2O-10% D2O, 100% D2O | 10 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0 | 6.0 | ambient | 268 | |
3 | DQF-COSY | 0.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.0 | 90% H2O-10% D2O, 100% D2O | 10 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0 | 6.0 | ambient | 268 | |
4 | H-P Cosy, COSY-45, T1 measurement, Translational diffusion constant measurement | 0.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.0 | 90% H2O-10% D2O, 100% D2O | 10 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0 | 6.0 | ambient | 268 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 600 |
2 | Bruker | AMX | 600 |
NMR Refinement | ||
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Method | Details | Software |
distance geometry, simulated annealing, restrained molecular dynamics | the structure calculation was based on a total of 316 restraints, 258 NOE-derived distance constraints, 40 of dihedral angle restraints, and 18 distance restraints from hydrogen bonds of Wason-Creek base pairs. | UXNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy |
Conformers Calculated Total Number | 9 |
Conformers Submitted Total Number | 9 |
Representative Model | 1 (closest to the average) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear and heteronuclear (1H-31P) techniques. Diffusion constant measurement experiment was used to address the conformation of the complex adopting either homoduplex or self-folded hairpin form. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | UXNMR | Aspect X32 | Bruker |
2 | processing | Felix | 98 and 2000 | Accelrys |
3 | structure solution | X-PLOR | 3.851 | Axel T. Brunger |
4 | data analysis | MARDIGRAS | 3.0 | Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar |
5 | refinement | X-PLOR | 3.851 | Axel T. Brunger |