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 42: Line 42:
 
!PDB-ID || Resolution (Å) || Chain || Covered residues || Missing residues || R-Value(obs.) || R-Free || pH || Temperature (K)
 
!PDB-ID || Resolution (Å) || Chain || Covered residues || Missing residues || R-Value(obs.) || R-Free || pH || Temperature (K)
 
|-
 
|-
|[http://www.pdb.org/pdb/files/2NT0.pdb 2NT0] || 1.79 || A/B/C/D || 40-536 (92.7%) || 1-39? || 0.181 || 0.215 || 4.5 || 100
+
|[http://www.pdb.org/pdb/files/2NT0.pdb 2NT0] || '''1.79''' || A/B/C/D || 40-536 (92.7%) || 1-39? || 0.181 || 0.215 || 4.5 || 100
 
|-
 
|-
 
|[http://www.pdb.org/pdb/files/3GXI.pdb 3GXI] || 1.84 || A/B/C/D || 40-536 (92.7%) || 1-39? || 0.193 || 0.231 || 5.5 || ?
 
|[http://www.pdb.org/pdb/files/3GXI.pdb 3GXI] || 1.84 || A/B/C/D || 40-536 (92.7%) || 1-39? || 0.193 || 0.231 || 5.5 || ?
 
|-
 
|-
|[http://www.pdb.org/pdb/files/2V3F.pdb 2V3F] || 1.95 || A/B || 40-536 (92.7%) || 1-39? || 0.154 || 0.196 || '''6.5''' || 100
+
|[http://www.pdb.org/pdb/files/2V3F.pdb 2V3F] || 1.95 || A/B || 40-536 (92.7%) || 1-39? || '''0.154''' || '''0.196''' || '''6.5''' || 100
 
|-
 
|-
 
|[http://www.pdb.org/pdb/files/2V3D.pdb 2V3D] || 1.96 || A/B || 40-536 (92.7%) || 1-39? || 0.157 || 0.208 || '''6.5''' || 100
 
|[http://www.pdb.org/pdb/files/2V3D.pdb 2V3D] || 1.96 || A/B || 40-536 (92.7%) || 1-39? || 0.157 || 0.208 || '''6.5''' || 100

Revision as of 13:55, 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 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
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!)

Sources

PDB R-value and R-free