Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking
SOLUTION NMR - THEORETICAL MODEL
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | TROSY | 10% D2O/90% WATER | 10MM TRIS/HCL | 7.6 | 1 atm | 296 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| THE DEPOSITED STRUCTURE IS THE RESULT OF A HETERONUCLEAR NMR EXPERIMENT AND DOCKING SIMULATIONS. THE FINAL RESULT WAS MINIMIZED BY MOLECULAR DYNAMIC MINIMIZATION. | X-PLOR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | LEAST SHIFT VARIATION VIOLATION |
| Conformers Calculated Total Number | 1000 |
| Conformers Submitted Total Number | 1 |
| Additional NMR Experimental Information | |
|---|---|
| Details | COMBINED DOCKING AND NMR FILTERING SOLUTION. THE TROSY EXPERIMENT WAS PERFORMED ON THE 15N-LABELED CYTOCHROME WITH SUBSEQUENTLY ADDING OF THE HYDROGENASE. THE RESIDUES HAVING THE STRONGEST SHIFTS WERE USED TO FILTER THE DOCKING SOLUTIONS.THE AMINO-ACIDS ALA E5, CYS E10, HIS E14, GLY E15, ALA E16, ALA E22, GLY E24, VAL E29, GLN E32, LYS E54, ASN E59, ALA E60 OF THE CYTOCHROME C553 SHOW STRONGEST SHIFTS IN THE TROSY EXPERIMENTS. EACH TIME ONE OF THE AMINO ACIDS IS IN CONTACT (LESS THAN 5A IN THE COMPLEX) WITH ITS PARTNER ONE POINT IS ATTRIBUTED TO THE STRUCTURE. THEN THE ONE THOUSAND BEST STRUCTURES ARE RANKED ACCORDING TO THIS CRITERIUM AND THE 10 BEST SOLUTIONS ARE MINIMISED. A COMPARISON OF THESE SOLUTIONS GENERATES STRUCTURE WITH 5 IDENTICAL SOLUTIONS |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR | 3.843 | BRUNGER |
| 2 | structure solution | UXNMR | UXNMR | |
