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

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(Preparation)
(Preparation)
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<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.</caption>
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<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>
 
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Revision as of 09:02, 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 3HG3 is highlighted.

Entry Method Resolution (Å) Chain Positions PDBsum PDB R-factor
1R46 X-ray 3.25 A/B 32-429 ] ] 0.262
1R47 X-ray 3.45 A/B 32-429 ] ] 0.285
3GXN X-ray 3.01 A/B 32-429 ] ] 0.239
3GXP X-ray 2.20 A/B 32-429 ] ] 0.204
3GXT X-ray 2.70 A/B 32-429 ] ] 0.245
3HG2 X-ray 2.30 A/B 32-429 ] ] 0.178
3HG3 X-ray 1.90 A/B 32-429 ] ] 0.167
3HG4 X-ray 2.30 A/B 32-429 ] ] 0.166
3HG5 X-ray 2.30 A/B 32-429 ] ] 0.192
3LX9 X-ray 2.04 A/B 32-429 ] ] 0.178
3LXA X-ray 3.04 A/B 32-429 ] ] 0.216
3LXB X-ray 2.85 A/B 32-429 ] ] 0.227
3LXC X-ray 2.35 A/B 32-429 ] ] 0.186
3S5Y X-ray 2.10 A/B 32-429 ] ] 0.195
3S5Z X-ray 2.00 A/B 32-429 ] ] 0.211
3TV8 X-ray 2.64 A/B 32-429 ] ] 0.203

</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

Map all the 10 mutations onto the crystal structure.


Create mutation

SCWRL


Comparison energies

foldX

Minimise

Gromacs