2N3W

Solution structure of the Rpn1 T1 site with K48-linked diubiquitin in the contracted binding mode


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.3 mM [U-100% 15N] protein_1, 0.04-1.2 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide95% H2O/5% D2O506.7ambient298
22D 1H-15N HSQC0.08-0.3 mM protein_1, 0.3 mM [U-100% 15N] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide95% H2O/5% D2O506.7ambient298
32D 1H-13C HSQC aliphatic0.06-0.5 mM protein_1, 0.5 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide100% D2O506.7ambient298
42D 1H-13C HSQC aliphatic0.6 mM [U-13C] protein_1, 0.12-0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide100% D2O506.7ambient298
53D 1H-13C NOESY aliphatic0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide100% D2O506.7ambient298
63D 13C-half filter NOESY0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide100% D2O506.7ambient298
73D 13C-half filter NOESY0.5 mM protein_1, 0.5 mM [U-13C] protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide100% D2O506.7ambient298
84D HMQC-NOESY-HMQC0.6 mM [U-13C] protein_1, 0.6 mM protein_2, 50 mM HEPES, 50 mM sodium chloride, 2 mM DTT, 1 mM EDTA, 0.1 % sodium azide100% D2O506.7ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAvance850
NMR Refinement
MethodDetailsSoftware
simulated annealingTOPSPIN
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number50
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTOPSPINBruker Biospin
2processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3chemical shift assignmentXEASYBartels et al.
4data analysisXEASYBartels et al.
5peak pickingXEASYBartels et al.
6refinementX-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clore
7structure solutionX-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clore
8data analysisTALOSCornilescu, Delaglio and Bax
9data analysisProcheckNMRLaskowski and MacArthur