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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|[http://www.pdb.org/pdb/files/2V3D.pdb 2V3D] || 1.96 || A/B || 40-536 (92.7%) || A: 28-31, 499-503, B: -1-0, 498-503 || 0.157 || 0.208 || '''6.5''' || 100
 
|[http://www.pdb.org/pdb/files/2V3D.pdb 2V3D] || 1.96 || A/B || 40-536 (92.7%) || A: 28-31, 499-503, B: -1-0, 498-503 || 0.157 || 0.208 || '''6.5''' || 100
 
|-
 
|-
|[http://www.pdb.org/pdb/files/1OGS.pdb 1OGS] || 2.0 || A-/B || 40-536 (92.7%) || ? || 0.195 || 0.230 || 4.6 || 100
+
|[http://www.pdb.org/pdb/files/1OGS.pdb 1OGS] || 2.0 || A-/B || 40-536 (92.7%) || - || 0.195 || 0.230 || 4.6 || 100
 
|}
 
|}
 
<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>
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REMARK 465 THR B 502 <br/>
 
REMARK 465 THR B 502 <br/>
 
REMARK 465 MET B 503 <br/>
 
REMARK 465 MET B 503 <br/>
  +
  +
Our familiar reference structure, 1OGS, has no missing residues.
   
 
===2. Visualise the mutations you want to work with===
 
===2. Visualise the mutations you want to work with===

Revision as of 15:33, 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 (UniProt seq.) Missing residues (ATOM seq.) R-Value(obs.) R-Free pH Temperature (K)
2NT0 1.79 A/B/C/D 40-536 (92.7%) ? 0.181 0.215 4.5 100
3GXI 1.84 A/B/C/D 40-536 (92.7%) ? 0.193 0.231 5.5 ?
2V3F 1.95 A/B 40-536 (92.7%) A: 29-31, 499-503, B: -1-0, 27-32, 498-503 0.154 0.196 6.5 100
2V3D 1.96 A/B 40-536 (92.7%) A: 28-31, 499-503, B: -1-0, 498-503 0.157 0.208 6.5 100
1OGS 2.0 A-/B 40-536 (92.7%) - 0.195 0.230 4.6 100
Comparison of the resolution top five PDB structures according to different other criteria.

</figtable>

The 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

The next best candidate, 2V3D, has 9 residue gaps in chain A (one more than 2V3F) and 8 in chain B:

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 28
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 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

Our familiar reference structure, 1OGS, has no missing residues.

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