6OQ2
NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin
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 | 120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin | 95% H2O/5% D2O | 0 M | 6.8 | 1 atm | 298 | Bruker AVANCE III 600 |
2 | 2D 1H-15N HSQC | 100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin | 95% H2O/5% D2O | 0 M | 6.8 | 1 atm | 298 | Bruker AVANCE III 800 |
3 | 2D 1H-15N HSQC | 60 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin | 95% H2O/5% D2O | 0 M | 6.8 | 1 atm | 298 | Bruker AVANCE III 600 |
4 | 2D 1H-15N HSQC | 110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin | 95% H2O/5% D2O | 0 M | 6.8 | 1 atm | 298 | Bruker AVANCE III 800 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 800 |
2 | Bruker | AVANCE III | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | THE INITIAL HADDOCK INPUT WAS THE CRYSTAL STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN (PDB ID 6OQ1). AMBIGUOUS DISTANCE RESTRAINTS WERE FROM CHEMICAL SHIFT PERTURBATIONS AND DISTANCE RESTRAINTS WERE BASED ON PRES. | HADDOCK |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 400 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | TopSpin | Bruker Biospin | |
2 | peak picking | Sparky | Goddard | |
3 | refinement | HADDOCK | Bonvin | |
4 | structure calculation | HADDOCK | Bonvin |