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

From Bioinformatikpedia
(1. Choose a structure to work with)
(1. Choose a structure to work with)
Line 36: Line 36:
 
===1. Choose a structure to work with===
 
===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 [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 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">
 
<figtable id="structure_choice">
 
{|class="colBasic2"
 
{|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(obs.) || R-free || pH || Temperature (Kelvin)
 
|-
 
|-
|1OGS || 2.0 || A-/B || 40-536 || no || 0.195(obs.) || 0.230 || 4.60 || 100.0
+
|[http://www.pdb.org/pdb/files/1OGS.pdb | 1OGS] || 2.0 || A-/B || 40-536 || no || 0.195 || 0.230 || 4.6 || 100
 
|-
 
|-
|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH ||
+
|[http://www.pdb.org/pdb/files/2NT0.pdb | 2NT0] || 1.79 || A/B/C/D || 40-536 || Gaps || 0.181 || 0.215 || 4.5 || 100
 
|-
 
|-
|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH ||
+
|PDB-ID || Resolution (Å) || Chain || 40-536 || Gaps || R-factor || R-free || pH ||
 
|-
 
|-
|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH ||
+
|PDB-ID || Resolution (Å) || Chain || 40-536 || Gaps || R-factor || R-free || pH ||
 
|-
 
|-
|PDB-ID || Resolution (Å) || Chain || Positions || Gaps || R-factor || R-free || pH ||
+
|PDB-ID || Resolution (Å) || Chain || 40-536 || Gaps || R-factor || R-free || pH ||
 
|}
 
|}
 
<center><small>'''<caption>''' Comparison of the resolution top five PDB structures according to different other criteria.</caption></small></center>
 
<center><small>'''<caption>''' Comparison of the resolution top five PDB structures according to different other criteria.</caption></small></center>

Revision as of 14:20, 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;}

</css>

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 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.

</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!)