Solution NMR Structure of Protein ytfP from Escherichia coli. Northeast Structural Genomics Consortium Target ER111.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_15N-SEPARATED_NOESY | 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O | 100 mM NACL | 5.5 | AMBIENT | 293 | ||
| 2 | 3D_ 13C-SEPARATED_NOESY | 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O | 100 mM NACL | 5.5 | AMBIENT | 293 | ||
| 3 | 4D_13C- SEPARATED_NOESY | 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O | 100 mM NACL | 5.5 | AMBIENT | 293 | ||
| 4 | HNHA | 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O | 100 mM NACL | 5.5 | AMBIENT | 293 | ||
| 5 | HIGH RESOLUTION CH-HSQC | 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O | 100 mM NACL | 5.5 | AMBIENT | 293 | ||
| 6 | BACKBONE TR EXPTS | 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O | 100 mM NACL | 5.5 | AMBIENT | 293 | ||
| 7 | TOCSYS | 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O | 100 mM NACL | 5.5 | AMBIENT | 293 | ||
| 8 | HCCH COSY | 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O | 100 mM NACL | 5.5 | AMBIENT | 293 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| 2 | Varian | INOVA | 600 |
| 3 | Varian | INOVA | 750 |
| 4 | Varian | INOVA | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | THE STRUCTURES ARE BASED ON A TOTAL OF 1717 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 211 DIHEDRAL ANGLE CONSTRAINTS, AND 68 HYDROGEN BOND CONSTRAINTS (17.2 CONSTRAINTS PER RESIDUE; 6.9 LONG-RANGE CONSTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR). THE 10 LOWEST ENERGY STRUCTURES WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). | AUTOSTRUCTURE 2.1.0, XPLOR-NIH 2.0.6, CNS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | LOWEST ENERGY |
| Conformers Calculated Total Number | 56 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING HYPER AND TALOS.Completeness of NMR assignments: backbone, 97%; side chain, 91%; stereospecific methyl, 100%. Final structure quality factors for the ensemble, where ordered residues [S(PHI) + S(PSI) > 1.8] comprise 1-5,9-10,17-18,23-38,41-70,76-85,88-93,101-104,106-108: (a) RMSD for ordered residues: BB, 0.7; heavy atom, 1.2. (b) Ramachandran statistics for ordered residues: most favored: 89.9%; additionally allowed: 10.1%; generously allowed, 0.0%; disallowed, 0.0% (c) Procheck scores for ordered residues (raw/Z-): BB, -0.53/-1.77; all, -0.49/-2.90. (d) MAGE Molprobity clash score (raw/Z-): 28.47/-3.36. (e) RPF scores for goodness of fit to NOESY data: F-measure, 0.916; Recall, 0.962; Precision, 0.874; DP-score, 0.791. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | AUTOSTRUCTURE 2.1.0, XPLOR-NIH 2.0.6, CNS | 1.1 | HUANG, MONTELIONE (AUTOSTRUCTURE), SCHWIETERS, CLORE (XPLOR-NIH), BRUNGER (CNS) |
| 2 | structure solution | VNMR | 6.1C | |
| 3 | structure solution | PSVS | 1.0 | |
| 4 | structure solution | NMRPipe | 2.3 | |
| 5 | structure solution | Sparky | 3.91 | |
| 6 | structure solution | AutoAssign | 1.14 | |
| 7 | structure solution | HYPER | 3.2 | |
| 8 | structure solution | PdbStat | 3.27 | |
