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Electron density of MerA

Last update on the 7th of October, 2019

Here I study electron density of mercuric reductase (MerA) of Pseudomonas aeruginosa based on 1ZK7 PDB entry at resolution of 1.6 Å.

Electron density around the backbone

The electron density around the backbone was investigated at 3 significance levels: 1σ, 2σ, 3σ. The following template command was used to produce electron density surfaces at different significance levels: isomesh surface_name, 1zk7_map, sigma, backbone, 2.5, carve=2. See fig. 1.

Fig. 1. MerA backbone and electron density around it at diferent significance levels.

Inner parts of protein have an electron density of very good quality whereas the start (left part) and end (right part) have electron density of lower significance. The "free" region of protein in the centre of images is also of lower significance. However, the structure seems to be fitted good into the electron density map.

And a beautiful gif of surfaces :)

The inspection of one of inner alpha-helices has strengthen the conclusion about the quality of structure evaluation (fig. 2).

Fig. 2. 316-332 alpha-helix.

Electron density around residues

I selected 3 residues to investigate electron density around them (fig. 3).

Fig. 3. Electron density around selected residues at σ >= 2.

Residues seem to be placed in space at the great agreement with electron density map.

Conclusion

The inferred structure seems to reflect electron density decently.