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

From Bioinformatikpedia
(1. Choose a structure to work with)
(1. Choose a structure to work with)
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|[http://www.pdb.org/pdb/files/3GXI.pdb 3GXI] || 1.84 || A/B/C/D || 40-536 (92.7%) || ? || 0.193 || 0.231 || 5.5 || ?
 
|[http://www.pdb.org/pdb/files/3GXI.pdb 3GXI] || 1.84 || A/B/C/D || 40-536 (92.7%) || ? || 0.193 || 0.231 || 5.5 || ?
 
|-
 
|-
|[http://www.pdb.org/pdb/files/2V3F.pdb 2V3F] || 1.95 || A/B || 40-536 (92.7%) || 29-31, 499-503 (chain A) || '''0.154''' || '''0.196''' || '''6.5''' || 100
+
|[http://www.pdb.org/pdb/files/2V3F.pdb 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
 
|-
 
|-
|[http://www.pdb.org/pdb/files/2V3D.pdb 2V3D] || 1.96 || A/B || 40-536 (92.7%) || ? || 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
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</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:
+
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 <br/>
 
REMARK 465 MISSING RESIDUES <br/>
Line 85: Line 85:
 
REMARK 465 THR B 502 <br/>
 
REMARK 465 THR B 502 <br/>
 
REMARK 465 MET B 503 <br/>
 
REMARK 465 MET B 503 <br/>
  +
  +
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 <br/>
  +
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE <br/>
  +
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN <br/>
  +
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) <br/>
  +
REMARK 465 <br/>
  +
REMARK 465 M RES C SSSEQI <br/>
  +
REMARK 465 PRO A 28 <br/>
  +
REMARK 465 PRO A 29 <br/>
  +
REMARK 465 THR A 30 <br/>
  +
REMARK 465 PHE A 31 <br/>
  +
REMARK 465 LEU A 499 <br/>
  +
REMARK 465 VAL A 500 <br/>
  +
REMARK 465 ASP A 501 <br/>
  +
REMARK 465 THR A 502 <br/>
  +
REMARK 465 MET A 503 <br/>
  +
REMARK 465 GLU B -1 <br/>
  +
REMARK 465 PHE B 0 <br/>
  +
REMARK 465 LEU B 498 <br/>
  +
REMARK 465 LEU B 499 <br/>
  +
REMARK 465 VAL B 500 <br/>
  +
REMARK 465 ASP B 501 <br/>
  +
REMARK 465 THR B 502 <br/>
  +
REMARK 465 MET B 503 <br/>
   
 
===2. Visualise the mutations you want to work with===
 
===2. Visualise the mutations you want to work with===

Revision as of 14:27, 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

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