2JU4
NMR structure of the gamma subunit of cGMP phosphodiesterase
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.05 mM [U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
2 | 2D 1H-1H TOCSY | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
3 | 3D CBCA(CO)NH | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
4 | 3D HNCACB | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
5 | 2D 1H-1H TOCSY | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
6 | 3D HBHA(CO)NH | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
7 | 3D H(CCO)NH | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
8 | 3D C(CO)NH | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
9 | 3D HNCO | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
10 | 3D HNHA | 0.09 mM [U-100% 13C; U-100% 15N] PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
11 | 2D 1H-15N HSQC | 0.05 mM [U-15N] PROXYL-PDEgamma | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
12 | 2D 1H-15N HSQC | 0.05 mM [U-100% 15N] PROXYL-PDEgamma, 5 mM Ascorbic Acid | 93% H2O/7% D2O | 0 | 4 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 600 |
2 | Bruker | DMX | 750 |
3 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics, simulated annealing | There are 10272 close contacts in this entry. The deposited structures were calculated using the combined distance restraints derived from ten single PDEgamma mutants (in each mutant a native residue was replaced by the 3-maleimido-PROXYL-cysteine residue). As a result, the deposited structures contain 10 mutated residues which do not coexist in the process of NMR structure determination. To avoid the artificial steric hinderance between individual spin groups, the Van der Waals contacts involving the 2,2,5,5-tetramethyl-1-pyrrolidinyloxy group (but not the maleimide group) are turned off in the structure calculation. | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 100 |
Representative Model | 1 (fewest violations) |
Additional NMR Experimental Information | |
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Details | This protein is intrinsically disordered. Because the structures are largely disordered in solution, they contain several different conformational population. Therefore all the structures can not be superimposed. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | 2.4 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
2 | collection | VNMR | Varian | |
3 | processing | Sparky | 2.112 | Goddard |
4 | refinement | XPLOR-NIH | 2.11.2 | Schwieters, Kuszewski, Tjandra and Clore |