2K0M
Solution NMR structure of the uncharacterized protein from Rhodospirillum rubrum gene locus Rru_A0810. Northeast Structural Genomics Target RrR43
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 2 | 2D 1H-13C HSQC | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 3 | 3D HNCO | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 4 | 3D HNCA | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 5 | 3D HNCACB | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 6 | 3D HBHA(CO)NH | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 7 | 3D HCCH-COSY | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 8 | 3D HCCH-TOCSY | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 9 | 3D CCH-TOCSY | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 10 | 3D CBCA(CO)NH | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 11 | 3D 1H-15N NOESY | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 12 | 3D 1H-13C NOESY | 1.05 mM [U-100% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| 13 | 2D 1H-13C HSQC | 1.15 mM [U-5% 13C; U-100% 15N] RrR43, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 100 mM sodium chloride, 50 uM DSS, 5 mM calcium chloride | 90% H2O/10% D2O | 0.1 | 6.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | CYANA | |
| 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 | MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED. MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 94.7%, SIDECHAIN 93.1%, AROMATIC (SC) 100%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1727 NOE. MAX NOE VIOLATION 0.25 A (1MODEL). 6 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - 6-70, 75-94 (FOR [S(PHI)+S(PSI)] > 1.8) RMSD 0.6 BB, 1.0 ALL HEAVY ATOMS. SECONDARY STRUCTURE ELEMENTS ALPHA HELICES: (17-30, 39-50, 55-59), BETA STRANDS: (7-9, 12-14, 35-36, 63-70, 76-82, 87-89). RAMA. DISTRIBUTION: 90.2/9.7/0.1/0.1. PROCHECK (PSI-PHI): -0.29/-0.83 (RAW/Z), PROCHECK (ALL): -0.22/-1.30 (RAW/Z), MOLPROBITY CLASH: 15.46/-1.13 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.917, PRECISION: 0.895, F-MEASURE: 0.906, DP-SCORE: 0.738. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
| 2 | chemical shift assignment | AutoAssign | 2.4.0 | Zimmerman, Moseley, Kulikowski and Montelione |
| 3 | geometry optimization | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
| 4 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 5 | validation | PSVS | Bhattacharya and Montelione | |
| 6 | geometry optimization | TALOS | Cornilescu, Delaglio and Bax | |
| 7 | collection | TopSpin | 1.3 | Bruker Biospin |
| 8 | data analysis | Sparky | 3.112 | Goddard |
| 9 | visualization | MOLMOL | 2k2 | Koradi, Billeter and Wuthrich |
| 10 | refinement | ProcheckNMR | Laskowski and MacArthur | |
| 11 | validation | MolProbity | Richardson | |
