NMR structure of Ydj1 J-domain, a cytosolic Hsp40 from Saccharomyces cerevisiae
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 2 | 2D 1H-13C HSQC aliphatic | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 3 | 2D 1H-13C HSQC aromatic | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 4 | 3D HCCH-TOCSY | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 16 | 3D CBCA(CO)NH | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 800 | |
| 17 | 3D HNCACB | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 800 | |
| 18 | 3D HNCO | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 5 | 3D HBHA(CO)NH | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 10 | 3D C(CO)NH | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 9 | 3D H(CCO)NH | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 8 | 3D 1H-13C NOESY aliphatic | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Bruker AVANCE III 900 | |
| 7 | 3D 1H-13C NOESY aromatic | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Bruker AVANCE III 900 | |
| 13 | 2D 1H-15N HSQC | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 11 | 2D 1H-15N HSQC | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 279 | Varian VXRS 600 | |
| 12 | 2D 1H-15N HSQC | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 283 | Varian VXRS 600 | |
| 14 | 2D 1H-15N HSQC | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 283 | Bruker AVANCE III 600 | |
| 15 | 2D 1H-15N HSQC | 93% H2O/7% D2O | 150 NaCl mM | 7.5 | 1 atm | 283 | Bruker AVANCE III 600 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 900 |
| 2 | Varian | VXRS | 800 |
| 3 | Varian | VXRS | 600 |
| 4 | Bruker | AVANCE III | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Final step with explicit water refinement | PONDEROSA-C/S |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | Bruker Biospin | |
| 2 | collection | VNMR | Varian | |
| 3 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 4 | peak picking | NMRFAM-SPARKY | 1.41 | Lee, Tonelli and Markley |
| 5 | peak picking | APES | Shin, Lee and Lee | |
| 6 | chemical shift assignment | NMRFAM-SPARKY | 1.41 | Lee, Tonelli and Markley |
| 7 | chemical shift assignment | PINE | Bahrami, Markley, Assadi, and Eghbalnia | |
| 8 | chemical shift assignment | PINE-SPARKY | Lee, Westler, Bahrami, Eghbalnia and Markley | |
| 9 | structure calculation | PONDEROSA-C/S | Lee, Stark and Markley | |
| 10 | structure calculation | AUDANA | Lee, Petit, Cornilescu, Stark and Markley | |
| 11 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 12 | refinement | PONDEROSA-C/S | Lee, Stark and Markley | |
| 13 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
