i have one query. that if we have a multi domain protein structure to
solve ,and we know about only one small domain of the protein for MR .
other domain structure is not known then how we can proceed.
is there any procedure to utilize phase from the solution with known
domain .
Deleting the loop /unessential regions is a more robust way to go. You
will be surprise to see that how much those regions can contribute the
clashes. Increasing clash tolerance in Phaser makes the program runs
really slow and gives ambiguous results.
Best,
Nian
On Wed, Oct 21, 2009 at 11:41 PM,
I guess you know to test all likely space groups etc?
You can increase the number of permitted clashes - see the phaser GUI.
Or use molrep which has a more sophisticated way of checking for clashes..
Eleanor
Vandana Kukshal wrote:
hello
i have 3.25 A data of multidomain p
hello
i have 3.25 A data of multidomain protein with 4 individual domain
.one domains structure is already known . and for others domain 40 %
simmilar structure is known . when i am running phaser with one known
domain i am getting the solution but after getting solution i am
The same is true for Porphyridium purpureum
beta-CA and Halothiobacillus neapolitanus beta-CA. Both are composed of
pseudodimers composed of two structurally homologous domains. In the
case of H. neapolitanus, the domains have very little sequence
homology, and one domain has lost its active si
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Shankar Prasad Kanaujia
Sent: Thursday, July 02, 2009 12:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] multi-domain protein with identical tertiary structure
Dear CCP4 users,
Is there any multi-domain protein (with at lea
The cadmium-utilizing marine diatom carbonic anhydrase (CA) protein has
three consecutive CA domains that have very similar structures but
non-identical sequences.
See:
Structure and metal exchange in the cadmium carbonic anhydrase of marine
diatoms.
Xu Y, Feng L, Jeffrey PD, Shi Y, Morel FM.
Hi Shankar,
Another fascinating example might be Dscam (Down Syndrome cell adhesion
molecule) with multiple Ig like domains and Fibronectin type III domains.
Different splice isoforms are expressed in different nerves, and it serves
as a recognition module, same repels, different ones attract.
No
Savvas
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Shankar Prasad Kanaujia
Sent: Thursday, July 02, 2009 7:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] multi-domain protein with identical tertiary structure
Dear CCP4 users,
Is there any multi-domain
thank you all for quick answers.
-shankar
On Thu, Jul 2, 2009 at 12:47 PM, Charlie Bond wrote:
> Depending on your definition of 'identical', examples of repeated gene
> duplication contribute to these:
>
> You could look at glyoxalases where there are dimeric examples where each
> monomer is co
Depending on your definition of 'identical', examples of repeated gene
duplication contribute to these:
You could look at glyoxalases where there are dimeric examples where
each monomer is composed of a repeated subdomain (A1-A2:A1-A2) and
monomeric examples where a further duplication has occ
Hi Shankar,
If you mean what I think you mean - yes, hundreds - but it depends on
how strict you are about "identical'
Lots of proteins have repeat domains in them with the same fold (and
homologous sequence) and therefore very similar (if not quite
identical) tertiary structure.
Some examples i
Dear CCP4 users,
Is there any multi-domain protein (with at least two domains) which has
identical tertiary structure of each domain ?
Thanking you.
-regards
shankar
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