Difference between revisions of "Structure based mutation analysis of GBA"
From Bioinformatikpedia
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== Introduction == |
== Introduction == |
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| − | To carry out a structure-based analysis of the mutations chosen in [[Sequence_based_mutation_analysis_of_GBA#Introduction|Task 7]] a crystal structure had to be chosen. According to [http://www.uniprot.org/uniprot/P04062 Uniprot] 19 different crystal structures of glucocerebrosidase exist. The table below shows the six different structures with a resolution of or better than 2 Angstrom. 2NT0 is chosen as template for the analysis carried out in this section, as no residues are missing, the R-value is quite low, and it has the best resolution among the structures without missing residues. |
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| + | === Structure Selection === |
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| + | To carry out a structure-based analysis of the mutations chosen in [[Sequence_based_mutation_analysis_of_GBA#Introduction|Task 7]] a crystal structure had to be chosen. According to [http://www.uniprot.org/uniprot/P04062 Uniprot] 19 different crystal structures of glucocerebrosidase exist. The table below shows the six different structures with a resolution of or better than 2 Angstrom. 2NT0 is chosen as template for the analysis carried out in this section, as no residues are missing, the R-value is quite low, and it has the best resolution among the structures without missing residues. Only incomplete structures have been resolved near the physiological pH (7.4), therefore a structure resolved at a more acid pH had to be chosen. |
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!Missing Residues (A/B) |
!Missing Residues (A/B) |
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| − | |1OGS||2.00||0.195||||4.6|| |
+ | |1OGS||2.00||0.195||||4.6||0 |
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| + | |style="background: lightgray;"|2NT0||style="background: lightgray;"|1.79||style="background: lightgray;"|0.181||style="background: lightgray;"|.||style="background: lightgray;"|4.5||style="background: lightgray;"|0 |
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| − | |2NT0||''1.79''||0.181||||4.5||''0'' |
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|2V3D||1.96||0.157||||6.5||9/8 |
|2V3D||1.96||0.157||||6.5||9/8 |
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| − | |2V3E||2.00||0.163|||| |
+ | |2V3E||2.00||0.163||||7.5||7/7 |
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| − | |2V3F||1.95|| |
+ | |2V3F||1.95||0.154||||6.5||8/14 |
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| − | |3GXI||1.84||0.193||||NULL|| |
+ | |3GXI||1.84||0.193||||NULL||0 |
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Revision as of 14:03, 29 June 2011
Contents
Introduction
Structure Selection
To carry out a structure-based analysis of the mutations chosen in Task 7 a crystal structure had to be chosen. According to Uniprot 19 different crystal structures of glucocerebrosidase exist. The table below shows the six different structures with a resolution of or better than 2 Angstrom. 2NT0 is chosen as template for the analysis carried out in this section, as no residues are missing, the R-value is quite low, and it has the best resolution among the structures without missing residues. Only incomplete structures have been resolved near the physiological pH (7.4), therefore a structure resolved at a more acid pH had to be chosen.
| PDB ID | Resolution [Å] | R-factor | Coverage | pH | Missing Residues (A/B) |
|---|---|---|---|---|---|
| 1OGS | 2.00 | 0.195 | 4.6 | 0 | |
| 2NT0 | 1.79 | 0.181 | . | 4.5 | 0 |
| 2V3D | 1.96 | 0.157 | 6.5 | 9/8 | |
| 2V3E | 2.00 | 0.163 | 7.5 | 7/7 | |
| 2V3F | 1.95 | 0.154 | 6.5 | 8/14 | |
| 3GXI | 1.84 | 0.193 | NULL | 0 |
Mutations
TODO: create image and so on ...
