Difference between revisions of "Fabry:Structure-based mutation analysis"
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== Vizualisation == |
== Vizualisation == |
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[[File:FABRY_all.gif|300px|thumb|right|<caption>All SNPs mapped onto the structure 3HG3. Mutated sites are shown in blue. The active site (residues 170 and 231) is shown in pink, substrate binding site (position 203-207) in cyan and the existing five disulfide bonds (52 ↔ 94, 56 ↔ 63, 142 ↔ 172, 202 ↔ 223, 378 ↔ 382) are highlighted in yellow</caption>]] |
[[File:FABRY_all.gif|300px|thumb|right|<caption>All SNPs mapped onto the structure 3HG3. Mutated sites are shown in blue. The active site (residues 170 and 231) is shown in pink, substrate binding site (position 203-207) in cyan and the existing five disulfide bonds (52 ↔ 94, 56 ↔ 63, 142 ↔ 172, 202 ↔ 223, 378 ↔ 382) are highlighted in yellow</caption>]] |
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Revision as of 09:00, 21 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 did not choose to use the structure 3HG3, although it has the best resolution (1.90 Å) and the second best R-factor (see <xr id="tab:Prep"/>), 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>, since it has an Alanin at position 170 (part of the active site) instead of an Aspartic acid. After excluding those structures, that had deviations in the sequence, we had to choose between ten sequences (1R46, 1R47, 3GXN, 3GXP, 3GXT, 3HG2, 3HG4, 3HG5, 3S5Y, 3S5Z) and decided to use 3S5Y. This structure has the advantage of a good pH, very good coverage and still reasonable resolution and R-factor.
Vizualisation
Create mutation
SCWRL
