2LW4
Solution NMR Structure of Human Transcription Elongation Factor A protein 2, Central Domain, Northeast Structural Genomics Consortium (NESG) Target HR8682B
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] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
2 | 2D 1H-13C CT-HSQC aliphatic | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
3 | 3D HNCO | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
4 | 3D CBCA(CO)NH | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
5 | 3D HNCACB | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
6 | 3D HN(CA)CO | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
7 | 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
8 | 3D (H)C(CO)NH-TOCSY | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
9 | 3D HBHA(CO)NH | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
10 | 3D HCCH-TOCSY | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
11 | 2D 1H-13C CT-HSQC aromatic | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
12 | 3D (H)CCH-COSY aliphatic | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
13 | 1D 15N T1 | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
14 | 1D 15N T2 | 1.0 mM [U-100% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 | ||
15 | 2D 1H-13C CT-HSQC methyl | 1.0 mM [5% 13C; U-100% 15N] HR8682B.004, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM TRIS | 90% H2O/10% D2O | 7.5 | ambient | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 750 |
2 | Varian | INOVA | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD | CNS |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | target function |
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 | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
2 | structure solution | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
3 | geometry optimization | CNS | 1.2 | 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 | ASDP | 1.0 | Huang, Tejero, Powers and Montelione |
8 | refinement | ASDP | 1.0 | Huang, Tejero, Powers and Montelione |
9 | data analysis | XEASY | 1.3.13 | Bartels et al. |
10 | data analysis | CARA | 1.8.4 | Keller and Wuthrich |
11 | chemical shift assignment | CARA | 1.8.4 | Keller and Wuthrich |
12 | peak picking | CARA | 1.8.4 | Keller and Wuthrich |
13 | collection | VnmrJ | 2.2D | Varian |
14 | chemical shift assignment | PINE | 2.0 | Bahrami, Markley, Assadi, and Eghbalnia |
15 | geometry optimization | TALOS+ | Shen, Cornilescu, Delaglio and Bax | |
16 | structure validation | PSVS | Bhattacharya, Montelione |