1YH5
Solution NMR Structure of Protein yggU from Escherichia coli. Northeast Structural Genomics Consortium Target ER14.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D 15N-NOESY | 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 | 50 mM NACL | 6.5 | AMBIENT | 293 | ||
| 2 | 3D 13C-NOESY | 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 | 50 mM NACL | 6.5 | AMBIENT | 293 | ||
| 3 | 3D AROMATIC 13C-NOESY | 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 | 50 mM NACL | 6.5 | AMBIENT | 293 | ||
| 4 | 2D 15N | 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 | 50 mM NACL | 6.5 | AMBIENT | 293 | ||
| 5 | 1H HSQC-J | 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 | 50 mM NACL | 6.5 | AMBIENT | 293 | ||
| 6 | 2D 15N | 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 | 50 mM NACL | 6.5 | AMBIENT | 293 | ||
| 7 | 1H MEXICO | 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 | 50 mM NACL | 6.5 | AMBIENT | 293 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| 2 | Varian | INOVA | 600 |
| 3 | Varian | INOVA | 750 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| TORSION ANGLE DYNAMICS SIMULATED ANNEALING | THE STRUCTURE IS BASED ON A TOTAL OF 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (12.6 CONSTRAINTS PER RESIDUE; 4.1 LONG-RANGE CONTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE WITH XPLOR. | X-PLOR 2.0.4 (NIH), AUTOSTRUCTURE |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 56 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (n/a) |
| Additional NMR Experimental Information | |
|---|---|
| Details | THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING THE AUTOSTRUCTURE PROGRAM. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS.FINAL STRUCTURE QUALITY FACTORS FOR THE ENSEMBLE, WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 8-23,28-29,31-34,37-41,44-65,67-77,80-87: (A) RMSD FOR ORDERED RESIDUES: BB, 0.7 ANG; HEAVY ATOM, 1.2 ANG. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED: 75.9%; ADDITIONALLY ALLOWED: 23.0%; GENEROUSLY ALLOWED, 1.0%; DISALLOWED, 0.2% (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): BB, -1.14/-2.23; ALL, -1.0/-4.17. (D) MAGE MOLPROBITY CLASH SCORE (RAW/Z): 33.22/-4.18 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: F-MEASURE, 0.944; RECALL, 0.977; PRECISION, 0.802; DP-SCORE, 0.726. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR 2.0.4 (NIH), AUTOSTRUCTURE | 2.0.0 | BRUNGER (X-PLOR), HUANG (AUTOSTRUCTURE) |
| 2 | structure solution | VNMR 6.1B | 6.1B | |
| 3 | structure solution | NMRPipe | 2.1 | |
| 4 | structure solution | SPARKY | 3.106 | |
| 5 | structure solution | AUTOASSIGN | 1.9 | |
| 6 | structure solution | AUTOSTRUCTURE | 2.0.0 | |
| 7 | structure solution | HYPER | 2.70 | |
| 8 | structure solution | TALOS | 2.1 | |
| 9 | structure solution | PDBSTAT | 3.27 | |
| 10 | structure solution | XPLOR | 2.0.4 (NIH), PSVS 1.0 | |
