2KWV

Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D HNCACB1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
23D 1H-15N NOESY1-2 mM [U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
33D 1H-15N TOCSY1-2 mM [U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
43D 1H-13C NOESY1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
53D HCCH-COSY1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
62D 1H-15N HSQC1-2 mM [U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
72D 1H-13C HSQC1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
83D HNCACB4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
93D 1H-15N NOESY4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
103D 1H-15N TOCSY4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
113D 1H-13C NOESY4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
123D HCCH-COSY4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
132D 1H-15N HSQC4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
142D 1H-13C HSQC4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
153D 1H-13C-filtered-13C-edited NOESY1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
163D 1H-13C-filtered-13C-edited NOESY4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
173D 1H-13C-filtered-13C-edited NOESY1.0 mM DNA polymerase iota UBM1, 4 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
183D 1H-13C-AROMATIC NOESY1.0 mM DNA polymerase iota UBM1, 4 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide95% H2O/5% D2O0.1896.0ambient288
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
2BrukerAVANCE750
3BrukerAVANCE900
NMR Refinement
MethodDetailsSoftware
molecular dynamicsAmber
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number200
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementAmber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
2collectionTopSpin2.1Bruker Biospin
3processingTopSpin2.1Bruker Biospin
4geometry optimizationMOLMOL2k.2Koradi, Billeter and Wuthrich
5peak pickingUNIO'081.0.4T. Herrmann
6chemical shift assignmentUNIO'081.0.4T. Herrmann
7structure solutionUNIO'081.0.4T. Herrmann
8structure solutionDYANAGuntert, Braun and Wuthrich
9data analysisCARA1.8.4R. Keller
10chemical shift assignmentCARA1.8.4R. Keller