2JN0
Solution NMR structure of the ygdR protein from Escherichia coli. Northeast Structural Genomics target ER382A.
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] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 2 | 2D 1H-13C HSQC | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 3 | 3D HNCO | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 4 | 3D HNCACB | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 5 | 3D HBHA(CO)NH | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 6 | 3D 1H-15N NOESY | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 7 | 3D 1H-13C NOESY | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 8 | 3D HCCH-TOCSY | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 9 | 3D HN(COCA)CB | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 10 | 3D HCCH-COSY | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| 11 | 3D CCH-TOCSY | 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide | 0.1 | 6.5 | AMBIENT | 293 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | NOESY ASSIGNMENT MADE WITH ITERATIVE METHOD USING CNS, HYPER (DIHEDRAL) AND DYANA FOLLOWED BY NIH- XPLOR FOR SIMMULATED ANNEALING MD. CONVERGED STRUCTURES WERE FURTHER MINIMIZED USING CNS IN EXPLICIT H2O SHELL (NILGES PROTOCOL). FULL LENGTH SEQUENCE WAS CARRIED THROUGH THE REFINEMENT PROTOCOL. COORDINATES FROM DISORDERED REGIONS, INCLUDING HEXHIS TAG, WERE NOT REPORTED. STRUCTURE IS BASED ON 439 CONSTRAINTS (216 LONG RANGE), 43 DIHEDRAL AND 20 H-BOND. | CNSSOLVE |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. MONOMER IN SOLUTION BY NMR TC = 8.2 +/- 1.0 NS (1D T1/T1RHO +/- FIT STD). POSSIBLE CIS PEPTIDE RES. 20K-21P. COULD NOT BE ANAMBIGUOSLY ESTABLISHED DUE TO SPECTRAL OVERLAP. COORDINATES REPORTED FROM RESIDUE 4 TO 53 SECTION BASED ON ORDER PARAMETER. MANUAL RESONANCE ASSIGNMENT. 13C AND 15N EDITED NOESY WERE WERE ASSIGNED USING AUTOSTRUCTURE. DIHEDRAL ANGLE RESTRAINTS DETERMINED BY HYPER AND TALOS. ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 80.4%, SIDECHAIN 77.7%, AROMATIC (SC) 100%, VL METHYL STEREOSP. 80%. STRUCTURE QUALITY FACTOR PSVS 1.3: ORDERED RESIDUES RANGES B-STRAND (14-16, 6-9, 47-49, 22-24, 29-33, 39-43, 65, 50-51, 56-57) [S(PHI)+S(PSI)]>1.8. RMSD 0.6 BB, 1.1 ALL HEAVY ATOMS. RAMA: 84.1% MOST FAV, 13.6% ADDTL.ALL.,2.2% GEN. ALL.,0.1% DISALL. PROCHECK (PSI-PHI): 0.75/-2.64 (RAW/Z), PROCHECK (ALL): -0.6/-3.55 (RAW/Z), MOLPROBITY CLASH: 23.61/- 2.53 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.925, PRECISION: 0.916, F-MEASURE: 0.921, DP-SCORE: 0.731. MONOMER BY LIGHT SCATTERING |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | CNSSOLVE | 1.1 | BRUNGER, et. al. |
| 2 | refinement | X-PLOR | 2.11.2 | CLORE et. al. |
| 3 | refinement | PROCHECK NMR | 3.51 | LASKOWSKI, MACARTHUR |
| 4 | refinement | MolProbity | 3.01 | LOVELL, RICHARDSON ET. AL. |
| 5 | refinement | QUEEN | 1.1 | NABUURS, VUISTER |
| 6 | refinement | PSVS | 1.3 | BHATTACHARYA, MONTELIONE |
| 7 | structure solution | AutoStructure | 2.1.1 | |
| 8 | structure solution | NMRPipe | ||
| 9 | structure solution | Sparky | ||
| 10 | structure solution | MOLMOL | ||
| 11 | structure solution | CNS | ||
| 12 | structure solution | PROCHECK | ||
| 13 | structure solution | XPLOR-NIH | ||
| 14 | structure solution | DIANA | ||
| 15 | structure solution | QUEEN | 1.1 | |
