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

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(1. Choose a structure to work with)
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'''This page is under construction.'''
 
'''This page is under construction.'''
   
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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.
 
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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<figtable id="structure_choice">
{|
 
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{|class="colBasic2"
 
!PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH || Temperature (Kelvin)
 
!PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH || Temperature (Kelvin)
 
|-
 
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|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH
 
|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH
 
|}
 
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<center><small>'''<caption>''' Comparison of the resolution top five PDB structures according to different other criteria.</caption></small></center>
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</figtable>
   
 
===2. Visualise the mutations you want to work with===
 
===2. Visualise the mutations you want to work with===

Revision as of 14:03, 28 August 2013

<css>

table.colBasic2 { margin-left: auto; margin-right: auto; border: 1px solid black; border-collapse:collapse; }

.colBasic2 th,td { padding: 3px; border: 1px solid black; }

.colBasic2 td { text-align:left; }

/* for orange try #ff7f00 and #ffaa56 for blue try #005fbf and #aad4ff

maria's style blue: #adceff grey: #efefef

  • /

.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;}

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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.

<figtable id="structure_choice">

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
Comparison of the resolution top five PDB structures according to different other criteria.

</figtable>

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!)