Gaucher Disease: Task 09 - Lab Journal

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Revision as of 13:22, 28 August 2013 by Kalemanovm (talk | contribs) (1. Choose a structure to work with)


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This page is under construction.


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 Positions Gaps R-factor(obs.) R-free pH Temperature (Kelvin)
1OGS 2.0 A-/B 40-536 no 0.195 0.230 4.6 100
2NT0 1.79 A/B/C/D 40-536 Gaps 0.181 0.215 4.5 100
PDB-ID Resolution (Å) Chain 40-536 Gaps R-factor R-free pH
PDB-ID Resolution (Å) Chain 40-536 Gaps R-factor R-free pH
PDB-ID Resolution (Å) Chain 40-536 Gaps R-factor R-free pH
Comparison of the resolution top five PDB structures according to different other criteria.


2. Visualise the mutations you want to work with

3. Create mutated structures

Energy comparisons



Gromacs (optional task for those who love MD!)