Difference between revisions of "Gaucher Disease: Task 09 - Lab Journal"

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(1. Choose a structure to work with)
(1. Choose a structure to work with)
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<center><small>'''<caption>''' Comparison of the resolution top five PDB structures according to different other criteria.</caption></small></center>
 
<center><small>'''<caption>''' Comparison of the resolution top five PDB structures according to different other criteria.</caption></small></center>
 
</figtable>
 
</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:
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  +
REMARK 465 MISSING RESIDUES
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REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
  +
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
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REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
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REMARK 465
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REMARK 465 M RES C SSSEQI
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REMARK 465 PRO A 29
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REMARK 465 THR A 30
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REMARK 465 PHE A 31
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REMARK 465 LEU A 499
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REMARK 465 VAL A 500
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REMARK 465 ASP A 501
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REMARK 465 THR A 502
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REMARK 465 MET A 503
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REMARK 465 GLU B -1
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REMARK 465 PHE B 0
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REMARK 465 ASP B 27
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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
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REMARK 465 MET B 503
   
 
===2. Visualise the mutations you want to work with===
 
===2. Visualise the mutations you want to work with===

Revision as of 14:08, 28 August 2013

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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>

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

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