1J7P
Solution structure of Calcium calmodulin C-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 (C'CA 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 | 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 | |
5 | HNCOCA (C'HA coupled) | 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 the correct structure. Here a total of 305 backbone dipolar couplings are used to refine the backbone structure. Additionally, 35 sidechain dipolar couplings and 81 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 (0.26 A for backbone and 0.90 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 the 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 CBHB dipolar couplings were measure 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 |