Difference between revisions of "Fabry:Structure-based mutation analysis"
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== Preparation == |
== Preparation == |
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<figtable id="tab:Prep"> |
<figtable id="tab:Prep"> |
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<caption>All available PDB structures assigned to the Uniprot entry [http://www.uniprot.org/uniprot/P06280 P06280] along with the according Resolution,<br> Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3S5Y is highlighted.</caption> |
<caption>All available PDB structures assigned to the Uniprot entry [http://www.uniprot.org/uniprot/P06280 P06280] along with the according Resolution,<br> Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3S5Y is highlighted.</caption> |
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Revision as of 21:58, 20 June 2012
Contents
Preparation
<figtable id="tab:Prep">
All available PDB structures assigned to the Uniprot entry P06280 along with the according Resolution,
Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3S5Y is highlighted.
| Entry | Method | Resolution (Å) | Chain | Positions (up to 429) | R-factor | R-free | pH | PDBsum | PDB |
|---|---|---|---|---|---|---|---|---|---|
| 1R46 | X-ray | 3.25 | A/B | 32-422 | 0.262 | 0.301 | 8.0 | [»] | [»] |
| 1R47 | X-ray | 3.45 | A/B | 32-422 | 0.285 | 0.321 | 8.0 | [»] | [»] |
| 3GXN | X-ray | 3.01 | A/B | 32-421 | 0.239 | 0.301 | 4.5 | [»] | [»] |
| 3GXP | X-ray | 2.20 | A/B | 32-422 | 0.204 | 0.265 | 4.5 | [»] | [»] |
| 3GXT | X-ray | 2.70 | A/B | 32-422 | 0.245 | 0.306 | 4.5 | [»] | [»] |
| 3HG2 | X-ray | 2.30 | A/B | 32-422 | 0.178 | 0.202 | 4.6 | [»] | [»] |
| 3HG3 | X-ray | 1.90 | A/B | 32-426 | 0.167 | 0.197 | 6.5 | [»] | [»] |
| 3HG4 | X-ray | 2.30 | A/B | 32-423 | 0.166 | 0.221 | 4.6 | [»] | [»] |
| 3HG5 | X-ray | 2.30 | A/B | 32-422 | 0.192 | 0.227 | 4.6 | [»] | [»] |
| 3LX9 | X-ray | 2.04 | A/B | 32-422 | 0.178 | 0.218 | 6.5 | [»] | [»] |
| 3LXA | X-ray | 3.04 | A/B | 32-426 | 0.216 | 0.244 | 6.5 | [»] | [»] |
| 3LXB | X-ray | 2.85 | A/B | 32-427 | 0.227 | 0.264 | 6.5 | [»] | [»] |
| 3LXC | X-ray | 2.35 | A/B | 32-422 | 0.186 | 0.237 | 6.5 | [»] | [»] |
| 3S5Y | X-ray | 2.10 | A/B | 32-422 | 0.195 | 0.230 | 5.1 | [»] | [»] |
| 3S5Z | X-ray | 2.00 | A/B | 32-421 | 0.211 | 0.234 | 5.1 | [»] | [»] |
| 3TV8 | X-ray | 2.64 | A/B | 32-422 | 0.203 | 0.239 | 4.6 | [»] | [»] |
</figtable>
We chose to use the structure 3HG3, since it has the best resolution (1.90 Å) and the second best R-factor (see <xr id="tab:Prep"/>). The best R-factor, which is a measure of the agreement between the crystallographic model and the experimental X-ray diffraction data <ref>R-factor (crystallography) (May 17, 2012) http://en.wikipedia.org/wiki/R-factor_%28crystallography%29, June 20, 2012</ref>, could be achieved with the structure 3HG4, but it has a resolution of 2.30 Å and hence we decided to use 3HG3. All structures cover the protein completely except for the signal peptide from position 1 to 31.
Vizualisation
<figure id="fig:allSNPs">
</figure>
Create mutation
SCWRL
