1NY4
Solution structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Northeast Structural Genomics Consortium target JR19.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D 15N-NOESY, 3D 13C-NOESY (aliphatic and aromatic) | 1.0 MM JR19 U-15N,13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.5 | 5% D2O/95% H2O | 100 mM NaCl | 6.5 | ambient | 293 | |
| 2 | 4D_13C-separated_NOESY | 1.0 MM JR19 U-15N,13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.5 | D2O | 100 mM NaCl | 6.5 | ambient | 293 | |
| 3 | HNHA | 1.0 MM JR19 U-15N,13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.5 | 5% D2O/95% H2O | 100 mM NaCl | 6.5 | ambient | 293 | |
| 4 | high resolution 13C,1H-HSQC | 1.0 MM JR19 U-15N, 5%-13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.5 | 5% D2O/95% H2O | 100 mM NaCl | 6.5 | ambient | 293 | |
| 5 | H/D exchange | 1.0 MM JR19 U-15N,13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.5 | 5% D2O/95% H2O | 100 mM NaCl | 6.5 | ambient | 293 | |
| 6 | backbone TR experiments, and 3D TOCSYs | 1.0 MM JR19 U-15N,13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.5 | 5% D2O/95% H2O | 100 mM NaCl | 6.5 | ambient | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 800 |
| 2 | Varian | INOVA | 750 |
| 3 | Varian | INOVA | 750 |
| 4 | Varian | INOVA | 600 |
| 5 | Varian | INOVA | 500 |
| 6 | Varian | UNITY | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics | THE STRUCTURES ARE BASED ON A TOTAL OF 828 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE RESTRAINTS, 99 DIHEDRAL ANGLE RESTRAINTS, AND 28 HYDROGEN BOND RESTRAINTS. (13.5 CONSTRAINTS PER RESIDUE; 5.2 LONG-RANGE RESTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (DYANA). THE UNSTRUCTURED 11 RESIDUE C-TERMINAL TAG (AAALEHHHHHH) WAS INCLUDED IN THE STRUCTURE CALCULATIONS BUT IS OMITTED FROM THIS DEPOSITION. | VNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 56 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest target function) |
| Additional NMR Experimental Information | |
|---|---|
| Details | THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. Manual side chain assignments. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS. BACKBONE CONFORMATIONS FOR RESIDUES 1-3, 5-6, 18-20, 22-23, 34-35, 48-49, 57-71, ARE NOT WELL-DEFINED [S(PHI) + S(PSI) < 1.8] IN THIS SOLUTION NMR STRUCTURE. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1B | Varian |
| 2 | processing | NMRPipe | 2.1 | Delaglio |
| 3 | data analysis | Sparky | 3.106 | Goddard |
| 4 | data analysis | AutoAssign | 1.9 | Zimmerman, Moseley, Montelione |
| 5 | refinement | AutoStructure | 1.1.2 | Huang, Montelione |
| 6 | structure solution | HYPER | 3.2 | Tejero, Montelione |
| 7 | refinement | DYANA | 1.5 | Guntert |
| 8 | structure solution | PdbStat | 3.27 | Tejero, Montelione |
