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Showing posts with label DeepView. Show all posts
Showing posts with label DeepView. Show all posts

Monday, 7 March 2011

How many clearly different structures of NHase are reported as pdb files?

Another helpful thing that the Iterative Magic Fit function within DeepView can do is provide a numerical value (based on a RMS calculation) for the similarity of the three dimensionality of the enzymes being overlaid. After concentrating on enzymes which are clearly NHases, discarding structures which are clearly mutants of an existing structure (which is either obvious from the title or the combination of author and date of submission), you get left with 13 distinct pdb files [1AHJ, 1IRE, 1UGP, 1V29, 2AHJ, 2CYZ, 2CZ6, 2D0Q, 2DPP, 2QDY, 2ZPB, 3A8O and 3HHT]. I then IMFed every one of these against each other to get a matrix of values for similarity. Basically if they had a value of less than 0.5, they look pretty much the same, greater than 1 than they look noticeably different.
The results of this showed that ALL the iron centred enzymes have RMS of <0.5 with each other which is not entirely surprising since they are all from Rhodococcus species. They all have RMS of greater than 1 for all the cobalt centred enzymes. There are two distinctly different cobalt centred arrangements: the Pseudonocardia thermophila pair of 1IRE and IUGP, and the trio of Bacillus structures of 1V29, 2DPP and 3HHT. Within these groupings they have RMS of less than 0.5, and between the groupings RMS of greater than 1.
Effectively this says to me that there are three basic structures for NHase known currently- one iron based and two cobalt based. Below is an excerpt from a table holding all the results from these calculations which shows this clustering.
PDB ID

1.06
1.06

1.06
0.07
1.19
1.14
0.45
1.09
0.44
1.07
0.47
1.09
0.45
1.09
1.22
1.16
0.46
1.09
0.44
1.08
3A8O
0.47
1.11
3HHT
1.22
1.15

Thursday, 24 February 2011

3A8O vs 2QDY

I have been playing with Deepview which offers a handy function where you can overlay pdb files and the resulting structure is colour coded for alignment diversity. Blue indicates really not much at all. As I have mentioned before the pdb for the Rhodococcus species AJ270 is coded as 2QDY and that for Rhodococcus species N-771 is 3A8O. Overlaying these two shows almost everything is dark blue, apart from differences for the two post-translationally modified cysteines in the active site and one bit dangling off the end. So that would be very similar then. You can see the same sort of picture if you overlay these with the 2CYZ too.