Difference between revisions of "Gaucher Disease: Task 09 - Lab Journal"
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− | Structure 2V3F seems to be a good choice because of the highest pH-value and the lowest R-value and R-free. However, there are some < |
+ | Structure 2V3F seems to be a good choice because of the highest pH-value and the lowest R-value and R-free. However, there are some <br/>missing residues, 8 in chain A: |
===2. Visualise the mutations you want to work with=== |
===2. Visualise the mutations you want to work with=== |
Revision as of 14:12, 28 August 2013
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This page is under construction.
Contents
Preparation
1. Choose a structure to work with
In the former tasks, we worked with the reference structure 1OGS, because it has no gaps - but an offset of 39 residues at the N terminus, as all structures for our protein P04062 referenced in UniProt - and has a pretty low resolution of 2.0 Å. However, there are four other structures with a lower resolution (all resolved using the X-ray diffraction method). We compare 1OGS and those four structures for the resolution, coverage and gaps, R-factor, R-free and pH-value at which the structure was resolved in the following table.
<figtable id="structure_choice">
PDB-ID | Resolution (Å) | Chain | Covered residues | Missing residues | R-Value(obs.) | R-Free | pH | Temperature (K) |
---|---|---|---|---|---|---|---|---|
2NT0 | 1.79 | A/B/C/D | 40-536 (92.7%) | 1-39? | 0.181 | 0.215 | 4.5 | 100 |
3GXI | 1.84 | A/B/C/D | 40-536 (92.7%) | 1-39? | 0.193 | 0.231 | 5.5 | ? |
2V3F | 1.95 | A/B | 40-536 (92.7%) | 1-39? | 0.154 | 0.196 | 6.5 | 100 |
2V3D | 1.96 | A/B | 40-536 (92.7%) | 1-39? | 0.157 | 0.208 | 6.5 | 100 |
1OGS | 2.0 | A-/B | 40-536 (92.7%) | 1-39? | 0.195 | 0.230 | 4.6 | 100 |
</figtable>
Structure 2V3F seems to be a good choice because of the highest pH-value and the lowest R-value and R-free. However, there are some
missing residues, 8 in chain A: