Re: [ccp4bb] Right Handedness of Density

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CCP4bb <-- 2007 <-- March 2007 <-- 30 March 2007

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Subject: Re: Right Handedness of Density
From: "Green, Todd" green {- at -} CBSE {- dot -} UAB {- dot -} EDU
Date: 2007-03-30

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Date: 2007-03-31

Subject: Re: Right Handedness of Density
From: Debanu Das ddas {- at -} LBL {- dot -} GOV
Date: 2007-03-30

Hi,
If you have density for the protein and the DNA and the density for
the protein is correct and you see left-handed DNA density, then I
suppose you are seeing Z-DNA?

Doesn't seem like a problem of incorrect enantiomorph if your protein
density is fine. You can pull out a Z-DNA structure from the PDB and see
if you can get a fit into the density that you see and if it makes sense
you can then try to build an idealized Z-DNA based on the sequence you
used for crystallization.

Regards,
Debanu.

Green, Todd wrote:

> Hello Ruchi,
>
> I know that when you use non-crystallographic averaging there is a
> possibility of the starting with positive density and ending up with
> negative, the enantiomorph, or the negative enantiomorph density. In
> order to shift back to the correct phases you can apply a simple
> formula. This is the math that i recall:
>
> positive structure alpha
> negative structure alpha + 180
> enantiomorphic structure -alpha
> negative enantiomorphic structure -alpha + 180
>
> The recollection comes from a paper in methods in enzymology that i
> don't recall the author or year of at the moment.
>
> I know your case has nothing to do with averaging but the math should
> hold true. In this case, you can switch between the enantiomorphs by
> multiplying the phases by -1. I don't know if this holds a solution to
> your case. It may be worth a quick shot just to multiply the phase
> column by -1. I may be far off base here but i think i am correct.
> This of course is assuming that you have the correct space group and
> that you have the enantiomorphic phases.
>
> If i am totally off on this, someone please correct me. I'm really
> sticking my neck out late on a friday, eh!
>
> Good Luck-
> todd
>
>
> -----Original Message-----
> From: CCP4 bulletin board on behalf of Ruchi Anand
> Sent: Fri 3/30/2007 5:31 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Right Handedness of Density
>
> Dear All,
> We are working with a DNA binding protein with 4 Zn sites in in ASU.
> Using SnB and then CNS we were able to get a map using MAD phasing and
> could visualize the density for the double helix of the DNA but it was
> a left handed spiral instead of the usual right handed one. The space
> group which yielded the result was P3(2). We tried to flip the sites
> and change the space group to P3(1) but we are not able to generate a
> sensible map. Any advice regarding the best way to proceed will be
> very helpful. The resolution is around 3.2.
> Thanks
> Ruchi
>
>
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CCP4bb <-- 2007 <-- March 2007 <-- 30 March 2007

Previous message:
Subject: Re: Right Handedness of Density
From: "Green, Todd" green {- at -} CBSE {- dot -} UAB {- dot -} EDU
Date: 2007-03-30

Next message:
Subject: (bigger) fragment identification of limited proteolysis w/ mass-spec
From: Yong Tang liutang19 {- at -} GMAIL {- dot -} COM
Date: 2007-03-31