2JN8
Solution NMR structure of Q8ZRJ2 from Salmonella typhimurium. Northeast Structural Genomics target StR65.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| 2 | 2D 1H-13C HSQC | 1.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| 3 | 3D 1H-15N NOESY | 1.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| 4 | 3D 1H-13C NOESY | 1.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| 5 | 3D HCCH-COSY | 1.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| 6 | 3D HCCH-TOCSY | 1.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| 7 | 3D TR backbone expts | 1.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| 8 | 3D TR backbone expts | 1.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| 9 | high resolution 2D 1H-13C HSQC | 0.89 mM [U-5% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 | 6.5 | ambient | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 750 |
| 2 | Varian | INOVA | 600 |
| 3 | Bruker | AMX | 600 |
| 4 | Varian | INOVA | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | THE STRUCTURES ARE BASED ON A TOTAL OF 1218 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 128 DIHEDRAL ANGLE CONSTRAINTS, AND 84 HYDROGEN BOND CONSTRAINTS (13.1 CONSTRAINTS PER RESIDUE, 2.4 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 2 TO 110 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE N-TERMINAL MET AND UNSTRUCTURED C-TERMINUS OF THE PROTEIN (HHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. Coordinates for the following residues are not well determined (S(PHI) + S(PSI) < 1.8): 1-11,21-31,65-67,85-95,110-115. | VNMR |
| 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) |
| Additional NMR Experimental Information | |
|---|---|
| Details | THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 96.9%, SIDE CHAIN, 95.7%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 83.3%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 2 TO 110, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 12-20,32-64,68-84,96-109: (A) RMSD (ORDERED RESIDUES): BB, 0.8, HEAVY ATOM, 1.2. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 96.1%, ADDITIONALLY ALLOWED, 3.9%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.36/1.73, ALL, 0.19/1.12. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 19.96/-1.90. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.976, PRECISION, 0.913, F-MEASURE, 0.944, DP-SCORE, 0.762. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1C | Varian |
| 2 | collection | Bruker | XWINNMR 3.5pl6 | Bruker |
| 3 | data analysis | AutoAssign | 2.2.1 | Zimmerman, Moseley, Kulikowski, Montelione |
| 4 | processing | Sparky | 3.110 | Goddard |
| 5 | data analysis | Sparky | 3.110 | Goddard |
| 6 | processing | NMRPipe | 2.3 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 7 | structure solution | AutoStructure | 2.1.1 | Huang, Tejero, Powers and Montelione |
| 8 | refinement | AutoStructure | 2.1.1 | Huang, Tejero, Powers and Montelione |
| 9 | refinement | X-PLOR NIH | 2.11.2 | Schwieters, Kuszewski, Tjandra and Clore |
| 10 | refinement | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 11 | data analysis | PdbStat | 4.1 | Tejero and Montelione |
| 12 | data analysis | PSVS | 1.3 | Bhattacharya, Hang and Montelione |
