Difference between revisions of "Gaucher Disease: Task 09 - Lab Journal"

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(Created page with "'''This page is under construction.''' ==Preparation== ===1. Choose a structure to work with=== ===2. Visualise the mutations you want to work with=== ===3. Create mutated …")
 
(1. Choose a structure to work with)
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===1. Choose a structure to work with===
 
===1. Choose a structure to work with===
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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 [[http://www.uniprot.org/uniprot/P04062 | 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 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.
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{|
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!PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH || Temperature (Kelvin)
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|-
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|1OGS || 2.0 || A-/B || 40-536 || no || 0.195(obs.) || 0.230 || 4.60 || 100.0
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|-
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|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH
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|-
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|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH
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|-
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|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH
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|-
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|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH
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|}
   
 
===2. Visualise the mutations you want to work with===
 
===2. Visualise the mutations you want to work with===

Revision as of 14:00, 28 August 2013

This page is under construction.

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 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.

PDB-ID Resolution (Å) Chain Positions Gaps R-factor R-free pH Temperature (Kelvin)
1OGS 2.0 A-/B 40-536 no 0.195(obs.) 0.230 4.60 100.0
PDB-ID Resolution (Å) Chain Positions Gaps R-factor R-free pH
PDB-ID Resolution (Å) Chain Positions Gaps R-factor R-free pH
PDB-ID Resolution (Å) Chain Positions Gaps R-factor R-free pH
PDB-ID Resolution (Å) Chain Positions Gaps R-factor R-free pH

2. Visualise the mutations you want to work with

3. Create mutated structures

Energy comparisons

foldX

Minimise

Gromacs (optional task for those who love MD!)