NMR Structure of the Rpa2829 protein from Rhodopseudomonas palustris: Northeast Structural Genomics Target RpR43
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 4D_13C-separated_NOESY | 1.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O | 95% H2O; 10% D2O | 100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate | 4.5 | ambient | 293 | |
| 2 | 3D_13C-separated_NOESY | 1.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O | 95% H2O; 10% D2O | 100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate | 5.0 | ambient | 293 | |
| 3 | 3D_15N-separated_NOESY | 1.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O | 95% H2O; 10% D2O | 100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate | 5.0 | ambient | 293 | |
| 4 | HNHA | 1.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O | 95% H2O; 10% D2O | 100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate | 5.0 | ambient | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 800 |
| 2 | Varian | INOVA | 750 |
| 3 | Varian | INOVA | 600 |
| 4 | Varian | UNITYPLUS | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| The initial structure was determined using automated structure determination (AutoStructure) and refined manually. A final refinement used simultated annealing in explicit solvent. | THE STRUCTURES ARE BASED ON A TOTAL OF 1039 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: RESTRAINING DISTANCE RESTRAINTS: TOTAL = 864; INTRA-RESIDUE [I=J] = 160; SEQUENTIAL [(I-J)=1] = 225; MEDIUM RANGE [1<(I-J)<5] = 131; LONG RANGE [(I-J)>=5] = 348; HYDROGEN BOND RESTRAINTS = 72 (2 PER H-BOND); NUMBER OF RESTRAINING DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 8.2; DIHEDRAL-ANGLE RESTRAINTS = 103 (50 PHI, 52 PSI, 1 CHI-1); TOTAL NUMBER OF RESTRAINTS PER RESTRAINED RESIDUE = 8.9; NUMBER OF LONG RANGE NOE DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 3.0; NUMBER OF STRUCTURES COMPUTED = 30; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.0001 ANG = 26.8+/-6; AVERAGE R.M.S. DISTANCE VIOLATION = 0.005 +/- 0.001 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 39.MAXIMUM DISTANCE VIOLATION = 0.26 ANG; AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.0001 DEG = 3.3+/-1.3; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 5; AVERAGE R.M.S. ANGLE VIOLATION = 0.42 +/- .01 DEG.; RMSD VALUES: BACKBONE ATOMS (N,C,C' RESIDUES 10-126) = 0.86 ANG, ALL HEAVY ATOMS = 1.52 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 33-126) = 0.68 ANG, ALL HEAVY ATOMS = 1.1.38 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 12-16,24-26,34-39,41-49,52-74,79-92,95-114,119-126) = 0.67 ANG,ALL HEAVY ATOMS = 1.19 ANG; PROCHECK (RESDIUES 10-126): MOST FAVORED REGIONS = 83.8%; ADDITIONAL ALLOWED REGIONS = 14.9%; GENEROUSLY ALLOWED REGIONS = 1.9%; DISALLOWED REGIONS = 0.4%. | VNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with lowest energy and fewest restraint violations |
| Conformers Calculated Total Number | 30 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (few violations and low energy and good geometery) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1C | Varian |
| 2 | processing | Felix | 98 | MSI/Accelerys |
| 3 | data analysis | Sparky | 3.106 | Tom Goddard, Tom James |
| 4 | structure solution | AutoStructure | 2.1.1 | Janet Huang, G.T. Montelione |
| 5 | refinement | X-PLOR | NIH-XPLOR | A. Brunger |
| 6 | refinement | CNS | 1.1 | A. Brunger |
