Difference between revisions of "Structure-based mutation analysis HEXA"

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(Sequence)
(Sequence)
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== Sequence ==
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== Sequence Description ==
   
We had to use a PDB file, in which are no missing residues. It was not possible to find one file, without any missing residues. In each file there was a gap between residue 74 to 89 and the last amino acid. Therefore, we decided to cut off the first 89 residues and use a PDB file with a structure from 89 - 528. This file can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/structure_pdb here]].
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We had to use a PDB file, in which are no missing residues and the quality of the structure should be high. We found only one PDB structure which was not bounded to a ligand. Therefore, we could not regard the quality and the pH value, the R-factor and the coverage. Nevertheless, we listed in the following table this values:
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  +
{| border="1" style="text-align:center; border-spacing:0;"
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|experiment type
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|X-Ray diffraction
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|-
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|Resolution
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|2.8 Å
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|-
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|temperature (Kelvin)
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|100K
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|-
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|temperature (Celsius)
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|-173°C
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|-
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|pH-Value
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|5.5 (slightly acid)
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|-
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|R-Value
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|0.270
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|-
  +
  +
It was not possible to find one file, without any missing residues. In each file there was a gap between residue 74 to 89 and the last amino acid. Therefore, we decided to cut off the first 89 residues and use a PDB file with a structure from 89 - 528. This file can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/structure_pdb here]].
   
 
== Mutations ==
 
== Mutations ==

Revision as of 13:38, 28 June 2011

Sequence Description

We had to use a PDB file, in which are no missing residues and the quality of the structure should be high. We found only one PDB structure which was not bounded to a ligand. Therefore, we could not regard the quality and the pH value, the R-factor and the coverage. Nevertheless, we listed in the following table this values:

It was not possible to find one file, without any missing residues. In each file there was a gap between residue 74 to 89 and the last amino acid. Therefore, we decided to cut off the first 89 residues and use a PDB file with a structure from 89 - 528. This file can be found [here].

Mutations

Because of the shorten PDB file, it was not possible for us to analyse the first two mutations on position 29 and 39.

experiment type X-Ray diffraction
Resolution 2.8 Å
temperature (Kelvin) 100K
temperature (Celsius)
pH-Value 5.5 (slightly acid)
R-Value 0.270
SNP-id codon number mutation codon mutation triplet
rs4777505 29 Asn -> Ser AAC -> AGC
rs121907979 39 Leu -> Arg CTT -> CGT
rs61731240 179 His -> Asp CAT -> GAT
rs121907974 211 Phe -> Ser TTC -> TCC
rs61747114 248 Leu -> Phe CTT -> TTT
rs1054374 293 Ser -> Ile AGT -> ATT
rs121907967 329 Trp -> TER TGG -> TAG
rs1800430 399 Asn -> Asp AAC -> GAC
rs121907982 436 Ile -> Val ATA -> GTA
rs121907968 485 Trp -> Arg gTGG -> CGG

Analysis of the mutations

We created for each mutation an extra page. The summary of the analysis can be seen in the Summary Section.