Solution structure of triheme cytochrome PpcA from Geobacter sulfurreducens reveals the structural origin of the redox-Bohr effect
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1 mM [U-100% 15N] CYTOCHROME C3-1, 1 mM PROTOPORPHYRIN IX CONTAINING FE-2, 45 mM sodium phosphate-3, 0.04 % sodium azide-4 | 93% H2O/7% D2O | 100 | 7.1 | AMBIENT | 298 | |
| 2 | 3D 1H-15N NOESY | 1 mM [U-100% 15N] CYTOCHROME C3-1, 1 mM PROTOPORPHYRIN IX CONTAINING FE-2, 45 mM sodium phosphate-3, 0.04 % sodium azide-4 | 93% H2O/7% D2O | 100 | 7.1 | AMBIENT | 298 | |
| 3 | 3D 1H-15N TOCSY | 1 mM [U-100% 15N] CYTOCHROME C3-1, 1 mM PROTOPORPHYRIN IX CONTAINING FE-2, 45 mM sodium phosphate-3, 0.04 % sodium azide-4 | 93% H2O/7% D2O | 100 | 7.1 | AMBIENT | 298 | |
| 4 | 2D 1H-1H TOCSY | 1 mM CYTOCHROME C3-5, 1 mM PROTOPORPHYRIN IX CONTAINING FE-6, 45 mM sodium phosphate-7, 0.04 % sodium azide-8 | 93% H2O/7% D2O | 100 | 7.1 | AMBIENT | 298 | |
| 5 | 2D 1H-1H NOESY | 1 mM CYTOCHROME C3-5, 1 mM PROTOPORPHYRIN IX CONTAINING FE-6, 45 mM sodium phosphate-7, 0.04 % sodium azide-8 | 93% H2O/7% D2O | 100 | 7.1 | AMBIENT | 298 | |
| 6 | 2D 1H-1H COSY | 1 mM CYTOCHROME C3-5, 1 mM PROTOPORPHYRIN IX CONTAINING FE-6, 45 mM sodium phosphate-7, 0.04 % sodium azide-8 | 93% H2O/7% D2O | 100 | 7.1 | AMBIENT | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | TopSpin | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | Bruker Biospin | |
| 2 | processing | TopSpin | Bruker Biospin | |
| 3 | chemical shift assignment | Sparky | Goddard | |
| 4 | structure solution calculation | PARADYANA | D.L.TURNER,L,BRENNAN,S.G.CHAMBERLIN, R.O.LOURO, A.V.XAVIER | |
| 5 | refinement | PARADYANA | D.L.TURNER,L,BRENNAN,S.G.CHAMBERLIN, R.O.LOURO, A.V.XAVIER | |
| 6 | superimposition | MOLMOL | Koradi, Billeter and Wuthrich | |
| 7 | visual inspection | MOLMOL | Koradi, Billeter and Wuthrich | |
| 8 | rms and mean structure calculations | MOLMOL | Koradi, Billeter and Wuthrich | |
| 9 | identification and classification of the consensus secondary structure | PROCHECKNMR | Laskowski and MacArthur | |
