2GB8
Solution structure of the complex between yeast iso-1-cytochrome c and yeast cytochrome c peroxidase
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 1H-15N HSQC | 0.3-0.4mM Cc(Fe3+)-CcP(Fe3+), 1:1 complex; 20mM NaPi, 100mM NaCl pH 6.0 | 20mM NaPi, 100mM NaCl pH 6.0 | 120mM | 6.0 | ambient | 301 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| rigid-body docking solely on the basis of experimental data; sidechain dynamics. | Coordinates of both proteins were taken from the PDB entry 2PCC. Sequences differ slightly from the experiment. Structure refinement was based on PRE-derived distance restraints for backbone atoms as a sole input. Only two energy terms, corresponding to restraints and van der Waals forces, are specified during the refinement procedure, which consist of two steps. First, a rigid-body docking of the protein molecules is carried out with van der Waals parameters for MTSL atoms set to zero. For each run performed, a single cluster of low-energy solutions is consistently produced. During the second step, 30 to 40 best structures are subjected to energy minimization and side-chain dynamics with fixed positions of backbone atoms for both proteins and active van der Waals parameters for MTSL. For the refined structures, the entire docking procedure is repeated until no further reduction in energy is observed. Best twenty structures of the final solution show an average rmsd from the lowest energy structure of 0.7 (0.2) Angstrom for the backbone atoms of cytochrome c after superposition of the peroxidase molecules. | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | Five single-cysteine CcP variants have been prepared and labelled with a paramagnetic spin-label. For each variant, two 2D [1H,15N] HSQC spectra were acquired, one of the complex between the spin-labelled protein and 15N Cc and the other of the control sample containing the complex of diamagnetically-labelled CcP with 15N Cc. From these, spin-label induced paramagnetic relaxation enhancements (PREs) of 15N Cc backbone amide resonances were determined and converted into intermolecular distance restraints, which were used for subsequent structure calculation of the protein complex. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 2.6 | Bruker |
| 2 | processing | Azara | 2.7 | W. Boucher |
| 3 | data analysis | ANSIG | 1.02 | M. Helgstrand, P.J. Kraulis, P. Allard, T. Hard |
| 4 | structure solution | XPLOR-NIH | 2.13 | C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clore |
| 5 | refinement | XPLOR-NIH | 2.13 | C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clore |
