6XN9
Solution NMR structure of recifin, a cysteine-rich tyrosyl-DNA Phosphodiesterase I modulatory peptide from the marine sponge Axinella sp.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 4 mg/mL recifin | 90% H2O/10% D2O | 0 mM | 4.85 | ambient atm | 298 | Bruker AVANCE III 600 |
2 | 2D 1H-1H TOCSY | 4 mg/mL recifin | 90% H2O/10% D2O | 0 mM | 4.85 | ambient atm | 298 | Bruker AVANCE III 600 |
3 | 2D 1H-1H NOESY | 4 mg/mL recifin | 100% D2O | 0 mM | 4.85 | ambient atm | 298 | Bruker AVANCE III 600 |
4 | 2D 1H-1H TOCSY | 4 mg/mL recifin | 100% D2O | 0 mM | 4.85 | ambient atm | 298 | Bruker AVANCE III 600 |
5 | 2D 1H-13C HSQC | 4 mg/mL recifin | 100% D2O | 0 mM | 4.85 | ambient atm | 298 | Bruker AVANCE III 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Structures calculated with erosion angle dynamics then refined and minimized in explicit water using Cartesian dynamics | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with acceptable covalent geometry |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 3.5 | Bruker Biospin |
2 | processing | TopSpin | 3.5 | Bruker Biospin |
3 | chemical shift assignment | CcpNmr Analysis | 2.4.1 | CCPN |
4 | data analysis | XEASY | Bartels et al. | |
5 | structure calculation | CYANA | 3.97 | Guntert, Mumenthaler and Wuthrich |
6 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read |