2KZ5
Solution NMR Structure of Transcription factor NF-E2 subunit's DNA binding domain from Homo sapiens, Northeast Structural Genomics Consortium Target HR4653B
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1.0 mM [U-100% 13C; U-100% 15N] HR4653B | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
| 2 | 2D 1H-13C HSQC | 1.1 mM [U-10% 13C; U-100% 15N] HR4653B | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
| 3 | 3D HNCO | 1.0 mM [U-100% 13C; U-100% 15N] HR4653B | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
| 4 | 3D CBCA(CO)NH | 1.0 mM [U-100% 13C; U-100% 15N] HR4653B | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
| 5 | 3D HNCACB | 1.0 mM [U-100% 13C; U-100% 15N] HR4653B | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
| 6 | 3D 1H-13C arom NOESY | 1.0 mM [U-100% 13C; U-100% 15N] HR4653B | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
| 7 | 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY | 1.0 mM [U-100% 13C; U-100% 15N] HR4653B | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
| 8 | 3D C(CO)NH | 1.0 mM [U-100% 13C; U-100% 15N] HR4653B | 95% H2O/5% D2O | 6.5 | ambient | 298 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics | CNS | |
| 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 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
| 2 | structure solution | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
| 3 | geometry optimization | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
| 4 | refinement | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
| 5 | geometry optimization | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
| 6 | structure solution | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
| 7 | data analysis,refinement | AutoStructure | 2.1 | Huang, Tejero, Powers and Montelione |
| 8 | data analysis | AutoAssign | 2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
| 9 | chemical shift assignment | AutoAssign | 2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
| 10 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 11 | data analysis | XEASY | Bartels et al. | |
| 12 | peak picking | XEASY | Bartels et al. | |
| 13 | chemical shift assignment | XEASY | Bartels et al. | |
| 14 | collection | TopSpin | Bruker Biospin | |
| 15 | collection | VnmrJ | Varian | |
| 16 | chemical shift assignment | PINE | Bahrami, Markley, Assadi, and Eghbalnia | |
| 17 | data analysis | Sparky | Goddard | |
| 18 | geometry optimization | TALOS+ | Shen, Cornilescu, Delaglio and Bax | |
| 19 | geometry optimization | PALES | PALES (Zweckstetter, Bax) | |
| 20 | geometry optimization | REDCAT | Valafar, Prestegard | |
