Pyridoxal Phosphatase Discussion: Difference between revisions
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'''PDB'''<BR> | |||
Based on the information obtained from '''PDB''', 2cfsA was identified to have the following features: <BR> | Based on the information obtained from '''PDB''', 2cfsA was identified to have the following features: <BR> | ||
* Isolated from ''Homo Sapiens'', and is expressed in ''Escherichia Coli''. <BR> | * Isolated from ''Homo Sapiens'', and is expressed in ''Escherichia Coli''. <BR> | ||
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* Resolution of 2.4 angstroms. The significance of this is that the probability that the number of side-chains in the wrong rotamer is relatively smaller. Proteins of similar resolution were noted also to: (1) have many small detectable errors, (2) be of correct folding, (3) contain fewer number of errors in the surface loops and (4) consist of visible water molecules and small ligands.<BR> | * Resolution of 2.4 angstroms. The significance of this is that the probability that the number of side-chains in the wrong rotamer is relatively smaller. Proteins of similar resolution were noted also to: (1) have many small detectable errors, (2) be of correct folding, (3) contain fewer number of errors in the surface loops and (4) consist of visible water molecules and small ligands.<BR> | ||
'''DALI''' <BR> | |||
A search on the protein in the '''Dali''' database yielded 176 hits, of which the top 11 were identified to be of potential significance on account of the information provided in the summary block of the results. The summary block provides the following information: <BR> | |||
* ''Z score'', or the statistical significance of the similarity between the hit protein and the protein-of-interest.<BR> | |||
* ''Root Mean Square Distance (RMSD)'', which indicates the degree of divergence between the hit protein and the protein-of-interest. <BR> | |||
* ''lali'', the total number of shared residues between the hit protein and the protein-of-interest. <BR> | |||
* ''nres'', or the total number of residues in the hit protein. <BR> | |||
* ''%id''. As the term implies, %id refers to the percentage of sequence identity over structurally identical positions. <BR> | |||
Function | Function | ||
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Revision as of 04:06, 31 May 2008
Evolution
Structure
PDB
Based on the information obtained from PDB, 2cfsA was identified to have the following features:
- Isolated from Homo Sapiens, and is expressed in Escherichia Coli.
- Structurally similar to the Pyridoxal Phosphate Phosphatase protein.
- Consists of a single type of chain (A), and (2) Magnesium components.
- Resolution of 2.4 angstroms. The significance of this is that the probability that the number of side-chains in the wrong rotamer is relatively smaller. Proteins of similar resolution were noted also to: (1) have many small detectable errors, (2) be of correct folding, (3) contain fewer number of errors in the surface loops and (4) consist of visible water molecules and small ligands.
DALI
A search on the protein in the Dali database yielded 176 hits, of which the top 11 were identified to be of potential significance on account of the information provided in the summary block of the results. The summary block provides the following information:
- Z score, or the statistical significance of the similarity between the hit protein and the protein-of-interest.
- Root Mean Square Distance (RMSD), which indicates the degree of divergence between the hit protein and the protein-of-interest.
- lali, the total number of shared residues between the hit protein and the protein-of-interest.
- nres, or the total number of residues in the hit protein.
- %id. As the term implies, %id refers to the percentage of sequence identity over structurally identical positions.
Function
