1J7O
Solution structure of Calcium-calmodulin N-terminal domain
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D HNCO (NH coupled) | 1mM calmodulin U-15N,13C; 100mM KCl, 16mM CaCl2, pH 7.0 | 95% H2O/5% D2O | 100mM KCl | 7.0 | ambient | 305 | |
2 | 3D HNCO (COCA coupled) | 1mM calmodulin U-15N,13C; 100mM KCl, 16mM CaCl2, pH 7.0 | 95% H2O/5% D2O | 100mM KCl | 7.0 | ambient | 305 | |
3 | CBCA(CO)NH (Quantitative J) | 1mM calmodulin U-15N,13C; 100mM KCl, 16mM CaCl2, pH 7.0 | 95% H2O/5% D2O | 100mM KCl | 7.0 | ambient | 305 | |
4 | HNCOCA (COHA coupled) | 1mM calmodulin U-15N,13C; 100mM KCl, 16mM CaCl2, pH 7.0 | 95% H2O/5% D2O | 100mM KCl | 7.0 | ambient | 305 | |
5 | 3D TROSY-HNCO (Quantitative J) | 1mM calmodulin U-15N,13C; 100mM KCl, 16mM CaCl2, pH 7.0 | 95% H2O/5% D2O | 100mM KCl | 7.0 | ambient | 305 | |
6 | 3D 13C-separated NOESY | 1mM calmodulin U-15N,13C; 100mM KCl, 16mM CaCl2, pH 7.0 | 95% H2O/5% D2O | 100mM KCl | 7.0 | ambient | 305 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 500 |
2 | Bruker | AVANCE | 600 |
3 | Bruker | AVANCE | 750 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | This structure is determined mainly by residual dipolar couplings measured in A liquid crystalline Pf1 medium. The structure calculation scheme, described in the paper, is based on the idea of refining existing structural models against dipolar couplings to derive thecorrect structure. Here a total of 323 backbone dipolar couplings are used to refine the backbone structure. Additionally, 38 sidechain dipolar couplings and 85 3-bond J couplings are used to determine the sidechain chi1 and chi2 rotamers as well as the presence of rotameric averaging. A total of three structures (model 1-3) were calculated starting from the 1. A crystal structure of Ca-calmodulin (PDB entry 1EXR), the NMR structure of apo-calmodulin (1F70), and the crystal structure of Ca-ligated parvalbumin (1CDP). The convergence of refinement is indicated by the small average RMSD between the three calculated structures and the average coordinates (0.28 A for backbone and 0.87 for all heavy atoms). During the three-stage simulated annealing described in the paper, restraints are included for most previously established hydrogen bonds, but have only minute effects (< 0.3 A) on the final structure. | X-PLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structure with lowest dipolar energy |
Conformers Calculated Total Number | 3 |
Conformers Submitted Total Number | 3 |
Representative Model | 2 (lowest dipolar energy) |
Additional NMR Experimental Information | |
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Details | A total of five sets of dipolar couplings are measured, including the one-bond NH, CAHA, C'CA, and NC' couplings, and the two-bond C'HA couplings. Additionally, the sidechain CBHB dipolar couplings are measured to assign chi-1 rotamers for locked sidechains. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | 3.851 | Brunger |
2 | processing | NMRPipe | 2.0 | Delaglio |