Difference between revisions of "Fabry:Structure-based mutation analysis"

From Bioinformatikpedia
(→‎Preparation)
(→‎Preparation)
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<div style="float:left; border:thin solid lightgrey; margin: 0px 20px 0px 0px;">
  
<div style="float:left; border:thin solid lightgrey; margin: 0px 20px 0px 0px;">
 
<figtable id="tab:Prep">
  
<figtable id="tab:Prep">
−
<caption>All available PDB structures assigned to the Uniprot entry [http://www.uniprot.org/uniprot/P06280 P06280] along with the according Resolution,<br> Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3HG3 is highlighted.</caption>
 +
<caption>All available PDB structures assigned to the Uniprot entry [http://www.uniprot.org/uniprot/P06280 P06280] along with the according Resolution,<br> Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3S5Y is highlighted.</caption>
 
{| class="wikitable sortable" style="border-collapse: collapse; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
  
{| class="wikitable sortable" style="border-collapse: collapse; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
 
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Entry
  
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Entry
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXC [»]]
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXC [»]]
 
|-
  
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3S5Y
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''3S5Y'''
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''X-ray'''
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.10
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''2.10'''
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''A/B'''
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''32-422'''
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.195
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''0.195'''
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.230
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''0.230'''
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 5.1
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''5.1'''
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3S5Y [»]]
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3S5Y [»]]
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3S5Y [»]]
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3S5Y [»]]

Revision as of 21:57, 20 June 2012

Preparation

<figtable id="tab:Prep"> All available PDB structures assigned to the Uniprot entry P06280 along with the according Resolution,
Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3S5Y is highlighted.

Entry Method Resolution (Å) Chain Positions (up to 429) R-factor R-free pH PDBsum PDB
1R46 X-ray 3.25 A/B 32-422 0.262 0.301 8.0 [»] [»]
1R47 X-ray 3.45 A/B 32-422 0.285 0.321 8.0 [»] [»]
3GXN X-ray 3.01 A/B 32-421 0.239 0.301 4.5 [»] [»]
3GXP X-ray 2.20 A/B 32-422 0.204 0.265 4.5 [»] [»]
3GXT X-ray 2.70 A/B 32-422 0.245 0.306 4.5 [»] [»]
3HG2 X-ray 2.30 A/B 32-422 0.178 0.202 4.6 [»] [»]
3HG3 X-ray 1.90 A/B 32-426 0.167 0.197 6.5 [»] [»]
3HG4 X-ray 2.30 A/B 32-423 0.166 0.221 4.6 [»] [»]
3HG5 X-ray 2.30 A/B 32-422 0.192 0.227 4.6 [»] [»]
3LX9 X-ray 2.04 A/B 32-422 0.178 0.218 6.5 [»] [»]
3LXA X-ray 3.04 A/B 32-426 0.216 0.244 6.5 [»] [»]
3LXB X-ray 2.85 A/B 32-427 0.227 0.264 6.5 [»] [»]
3LXC X-ray 2.35 A/B 32-422 0.186 0.237 6.5 [»] [»]
3S5Y X-ray 2.10 A/B 32-422 0.195 0.230 5.1 [»] [»]
3S5Z X-ray 2.00 A/B 32-421 0.211 0.234 5.1 [»] [»]
3TV8 X-ray 2.64 A/B 32-422 0.203 0.239 4.6 [»] [»]

</figtable>

We chose to use the structure 3HG3, since it has the best resolution (1.90 Å) and the second best R-factor (see <xr id="tab:Prep"/>). The best R-factor, which is a measure of the agreement between the crystallographic model and the experimental X-ray diffraction data <ref>R-factor (crystallography) (May 17, 2012‎) http://en.wikipedia.org/wiki/R-factor_%28crystallography%29, June 20, 2012</ref>, could be achieved with the structure 3HG4, but it has a resolution of 2.30 Å and hence we decided to use 3HG3. All structures cover the protein completely except for the signal peptide from position 1 to 31.

Vizualisation

<figure id="fig:allSNPs">

All SNPs mapped onto the structure 3HG3. Mutated sites are shown in blue. The active site (residues 170 and 231) is shown in pink, substrate binding site (position 203-207) in cyan and the existing five disulfide bonds (52 ↔ 94, 56 ↔ 63, 142 ↔ 172, 202 ↔ 223, 378 ↔ 382) are highlighted in yellow

</figure>


Create mutation

SCWRL


Comparison energies

foldX

Minimise

Gromacs

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