Dominant form of the low-affinity complex of yeast cytochrome c and cytochrome c peroxidase
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 0.4 mM [U-2H; U-15N] CcP, 0.4 mM Cc, 0.4 mM Cc1, 20 mM sodium phosphate | 93% H2O/7% D2O | 15 | 6.0 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | Uniform NMR System | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | AUTHORS STATE THAT CCP (CHAIN A) HAS TWO BINDING SITES FOR CC (CHAINS B AND C). ONE OF THE SITES IS BLOCKED BY PREPARING A COVALENT CCP-CC CROSSLINK (CHAINS A-B), WHILE STUDYING THE BINDING OF THE SECOND CC MOLECULE (CHAIN C) TO ANOTHER SITE. THE CROSS-LINKING WAS DONE VIA AN ENGINEERED DISULFIDE BETWEEN CCP V197C AND CC A81C GROUPS (I.E. CHAIN A V197C - CHAIN B A81C). IN ADDITION, THE NATIVE CYS RESIDUES OF BOTH CCP AND CC WERE MUTATED OUT (I.E. CHAIN A C128A AND CHAIN B C102T MUTATIONS). THE CROSSLINK STRUCTURE (CHAINS A-B), TAKEN FROM THE PDB ENTRY 1S6V, WAS KEPT FIXED IN THE NMR RESTRAINT-DRIVEN RIGID-BODY DOCKING OF THE SECOND CC MOLECULE (CHAIN C). RIGID-BODY REFINEMENT PROTOCOL IS DESCRIBED IN DETAIL IN THE MAIN CITATION ASSOCIATED WITH THIS ENTRY. | VnmrJ |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VnmrJ | Varian | |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | peak picking | CcpNMR | CCPN | |
| 4 | chemical shift assignment | CcpNMR | CCPN | |
| 5 | data analysis | CcpNMR | CCPN | |
| 6 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 7 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
