Difference between revisions of "Gaucher Disease: Task 09 - Lab Journal"
Kalemanovm (talk | contribs) (→1. Choose a structure to work with) |
Kalemanovm (talk | contribs) (→1. Choose a structure to work with) |
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Structure 2V3F seems to be a good choice because of the highest pH-value and the lowest R-value and R-free. However, there are some missing residues, 8 in chain A: |
Structure 2V3F seems to be a good choice because of the highest pH-value and the lowest R-value and R-free. However, there are some missing residues, 8 in chain A: |
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+ | |||
− | <nowiki> |
||
− | REMARK 465 MISSING RESIDUES </br> |
+ | REMARK 465 MISSING RESIDUES </br> |
− | REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE |
+ | REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE </br> |
− | REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN |
+ | REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN </br> |
− | REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) |
+ | REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) </br> |
− | REMARK 465 |
+ | REMARK 465 </br> |
− | REMARK 465 M RES C SSSEQI |
+ | REMARK 465 M RES C SSSEQI </br> |
− | REMARK 465 PRO A 29 |
+ | REMARK 465 PRO A 29 </br> |
− | REMARK 465 THR A 30 |
+ | REMARK 465 THR A 30 </br> |
− | REMARK 465 PHE A 31 |
+ | REMARK 465 PHE A 31 </br> |
− | REMARK 465 LEU A 499 |
+ | REMARK 465 LEU A 499 </br> |
− | REMARK 465 VAL A 500 |
+ | REMARK 465 VAL A 500 </br> |
− | REMARK 465 ASP A 501 |
+ | REMARK 465 ASP A 501 </br> |
− | REMARK 465 THR A 502 |
+ | REMARK 465 THR A 502 </br> |
− | REMARK 465 MET A 503 |
+ | REMARK 465 MET A 503 </br> |
− | REMARK 465 GLU B -1 |
+ | REMARK 465 GLU B -1 </br> |
− | REMARK 465 PHE B 0 |
+ | REMARK 465 PHE B 0 </br> |
− | REMARK 465 ASP B 27 |
+ | REMARK 465 ASP B 27 </br> |
− | REMARK 465 PRO B 28 |
+ | REMARK 465 PRO B 28 </br> |
− | REMARK 465 PRO B 29 |
+ | REMARK 465 PRO B 29 </br> |
− | REMARK 465 THR B 30 |
+ | REMARK 465 THR B 30 </br> |
− | REMARK 465 PHE B 31 |
+ | REMARK 465 PHE B 31 </br> |
− | REMARK 465 PRO B 32 |
+ | REMARK 465 PRO B 32 </br> |
− | REMARK 465 LEU B 498 |
+ | REMARK 465 LEU B 498 </br> |
− | REMARK 465 LEU B 499 |
+ | REMARK 465 LEU B 499 </br> |
− | REMARK 465 VAL B 500 |
+ | REMARK 465 VAL B 500 </br> |
− | REMARK 465 ASP B 501 |
+ | REMARK 465 ASP B 501 </br> |
− | REMARK 465 THR B 502 |
+ | REMARK 465 THR B 502 </br> |
− | REMARK 465 MET B 503 |
+ | REMARK 465 MET B 503 </br> |
− | </nowiki> |
||
===2. Visualise the mutations you want to work with=== |
===2. Visualise the mutations you want to work with=== |
Revision as of 15:11, 28 August 2013
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This page is under construction.
Contents
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 |
</figtable>
Structure 2V3F seems to be a good choice because of the highest pH-value and the lowest R-value and R-free. However, there are some missing residues, 8 in chain A:
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 PRO A 29
REMARK 465 THR A 30
REMARK 465 PHE A 31
REMARK 465 LEU A 499
REMARK 465 VAL A 500
REMARK 465 ASP A 501
REMARK 465 THR A 502
REMARK 465 MET A 503
REMARK 465 GLU B -1
REMARK 465 PHE B 0
REMARK 465 ASP B 27
REMARK 465 PRO B 28
REMARK 465 PRO B 29
REMARK 465 THR B 30
REMARK 465 PHE B 31
REMARK 465 PRO B 32
REMARK 465 LEU B 498
REMARK 465 LEU B 499
REMARK 465 VAL B 500
REMARK 465 ASP B 501
REMARK 465 THR B 502
REMARK 465 MET B 503