Difference between revisions of "Gaucher Disease: Task 09 - Lab Journal"
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− | In all the investigated structures residues numbered 1-497 are native and correspond to the positions 40-536 in the UniProt sequence P04062. In some of the structures, like in 2V3E, two residues were added at the beginning (EF, positions -1, 0) and six residues at the end (LLVDTM, positions 498-503). If these "axillary" residues are missing in the resolved structure, we can ignore it. |
+ | In all the investigated structures residues numbered 1-497 are native and correspond to the positions 40-536 in the UniProt sequence P04062. In some of the structures, like in 2V3E, two residues were added at the beginning (EF, positions -1, 0) and six residues at the end (LLVDTM, positions 498-503). If these "axillary" residues are missing in the resolved structure, we can ignore it. For this reason they are presented in brackets in the table. |
The structures '''2NT0''', '''3GXI''' and our familiar reference structure, '''1OGS''', have no missing residues and the first two candidates have the lowest resolutions (1.79 and 1.84, respectively). However, the pH-values, at which the structures were resolved, are too low (4.5, 5.5 and 4.6, respectively). |
The structures '''2NT0''', '''3GXI''' and our familiar reference structure, '''1OGS''', have no missing residues and the first two candidates have the lowest resolutions (1.79 and 1.84, respectively). However, the pH-values, at which the structures were resolved, are too low (4.5, 5.5 and 4.6, respectively). |
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REMARK 465 THR B 502 |
REMARK 465 THR B 502 |
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REMARK 465 MET B 503 --> |
REMARK 465 MET B 503 --> |
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− | Moreover, this structure has relatively low R-value (0.163) and R-free (0.220) values, which are lower than in 2NT0, 3GXI or 1OGS. As 2V3E is the lowest resolution structure resolved at a physiological pH-value and the chain B has no gaps, we choose '''2V3E, chain B''' |
+ | Moreover, this structure has relatively low R-value (0.163) and R-free (0.220) values, which are lower than in 2NT0, 3GXI or 1OGS. As 2V3E is the lowest resolution structure resolved at a physiological pH-value and the chain B has no gaps, we choose '''2V3E, chain B'''. |
===2. Visualise the mutations you want to work with=== |
===2. Visualise the mutations you want to work with=== |
Revision as of 18:56, 29 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 - except for an offset of 39 residues at the N terminus that all structures for our protein P04062 referenced in UniProt have - and has a pretty low resolution of 2.0 Å. However, there are five other structures with a lower or equal resolution (all resolved using the X-ray diffraction method). We compared 1OGS and those five structures for the resolution, coverage and gaps, R-factor, R-free and pH-value at which the structure was resolved in order to choose the best structure suiting the requirements of this task (<xr id="structure_choice"/>).
<figtable id="structure_choice">
PDB-ID | Resolution (Å) | Chain | Covered residues (UniProt seq.) | Missing residues (ATOM seq.) | Covered residues (ATOM seq.) | R-Value(obs.) | R-Free | pH | Temperature (K) |
---|---|---|---|---|---|---|---|---|---|
2NT0 | 1.79 | A/B/C/D | 40-536 (92.7%) | - | 1-497 | 0.181 | 0.215 | 4.5 | 100 |
3GXI | 1.84 | A/B/C/D | 40-536 (92.7%) | - | 1-497 | 0.193 | 0.231 | 5.5 | NULL |
2V3F | 1.95 | A/B | 40-536 (92.7%) | A: 29-31, (499-503), B: (-1-0), 27-32, (498-503) | A: -1-28, 32-498, B: 1-26, 33-497 | 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) | A: -1-27, 32-498, B: 1-497 | 0.157 | 0.208 | 6.5 | 100 |
2V3E | 2.0 | A/B | 40-536 (92.7%) | A: 31, (498-503), B: (-1), (498-503) | A: -1-30, 32-497, B: 0-497 | 0.163 | 0.220 | 7.5 | 100 |
1OGS | 2.0 | A/B | 40-536 (92.7%) | - | 1-497 | 0.195 | 0.230 | 4.6 | 100 |
</figtable>
In all the investigated structures residues numbered 1-497 are native and correspond to the positions 40-536 in the UniProt sequence P04062. In some of the structures, like in 2V3E, two residues were added at the beginning (EF, positions -1, 0) and six residues at the end (LLVDTM, positions 498-503). If these "axillary" residues are missing in the resolved structure, we can ignore it. For this reason they are presented in brackets in the table.
The structures 2NT0, 3GXI and our familiar reference structure, 1OGS, have no missing residues and the first two candidates have the lowest resolutions (1.79 and 1.84, respectively). However, the pH-values, at which the structures were resolved, are too low (4.5, 5.5 and 4.6, respectively).
The structure 2V3F seems to be a good choice, because it compromises between the pH-value (pH=6.5 is near to the physiological value of 7.4) and low resolution (1.95 Å). Moreover, it has the lowest R-value (0.154) and R-free (0.196). However, there are some missing residues (29-31 in chain A and 27-32 in chain B).
The candidate 2V3D has similar values, but it also has gaps in chain A (28-31). We could have used the chain B, thought.
A structure candidate with the same resolution as 1OGS and a neutral pH of 7.5 is 2V3E. It has only one missing residue in chain A (31) and none native residues are missing in chain B. Moreover, this structure has relatively low R-value (0.163) and R-free (0.220) values, which are lower than in 2NT0, 3GXI or 1OGS. As 2V3E is the lowest resolution structure resolved at a physiological pH-value and the chain B has no gaps, we choose 2V3E, chain B.