2KQZ

Solution structure of the Rpn13 DEUBAD domain


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
23D HNCA0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
33D HN(CO)CA0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
43D HNCO0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
53D HN(CO)CA0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
63D HCCH-TOCSY0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
72D 1H-15N HSQC0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
83D HNCACB0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
92D 1H-1H NOESY0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
102D 1H-1H NOESY1.0 mM XCCD100% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
112D 1H-13C HSQC0.7 mM [U-13C] XCCD100% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
123D 1H-13C NOESY0.7 mM [U-13C] XCCD100% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
132D 1H-15N HSQC0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
143D 1H-15N NOESY0.7 mM [U-100% 13C; U-100% 15N; U-70% 2H] XCCD, 0.7 mM [U-15N; U-50% 2H] XCCD, 0.7 mM [U-15N; 100% 2H] XCCD, 0.5 mM [U-15N] XCCD, 1.0 mM XCCD90% H2O/10% D2O20 mM phosphate, 50 mM NaCl6.5ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianINOVA600
2VarianINOVA800
3VarianINOVA900
NMR Refinement
MethodDetailsSoftware
simulated annealingThe structures are based on a total of 2721 restraints, 2503 are NOE-derived distance constraints, 76 distance restraints from hydrogen bonds, 142 dihedral angle restraints.VnmrJ
NMR Ensemble Information
Conformer Selection Criteriaall calculated structures submitted
Conformers Calculated Total Number35
Conformers Submitted Total Number35
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionVnmrJVarian
2processingNMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3chemical shift assignmentXEASY6.4Bartels et al.
4data analysisXEASY6.4Bartels et al.
5peak pickingXEASY6.4Bartels et al.
6chemical shift assignmentCARA1.8.4Keller and Wuthrich
7data analysisCARA1.8.4Keller and Wuthrich
8peak pickingCARA1.8.4Keller and Wuthrich
9refinementX-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clore
10structure solutionX-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clore