2JU4

NMR structure of the gamma subunit of cGMP phosphodiesterase


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.05 mM [U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
22D 1H-1H TOCSY0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
33D CBCA(CO)NH0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
43D HNCACB0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
52D 1H-1H TOCSY0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
63D HBHA(CO)NH0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
73D H(CCO)NH0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
83D C(CO)NH0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
93D HNCO0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
103D HNHA0.09 mM [U-100% 13C; U-100% 15N] PDEgamma90% H2O/10% D2O04ambient298
112D 1H-15N HSQC0.05 mM [U-15N] PROXYL-PDEgamma90% H2O/10% D2O04ambient298
122D 1H-15N HSQC0.05 mM [U-100% 15N] PROXYL-PDEgamma, 5 mM Ascorbic Acid93% H2O/7% D2O04ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDMX600
2BrukerDMX750
3VarianINOVA600
NMR Refinement
MethodDetailsSoftware
molecular dynamics, simulated annealingThere 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
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number200
Conformers Submitted Total Number100
Representative Model1 (fewest violations)
Additional NMR Experimental Information
DetailsThis 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
#ClassificationVersionSoftware NameAuthor
1processingNMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2collectionVNMRVarian
3processingSparky2.112Goddard
4refinementXPLOR-NIH2.11.2Schwieters, Kuszewski, Tjandra and Clore