Hi,
try SAVES online tool,and ProSa.
On Mon, 20 Dec, 2021, 9:40 pm Reza Khayat, wrote:
> Hi,
>
>
> Can anyone suggest how to validate a predicted structure? Something
> similar to wwPDB validation without the need for refinement statistics. I
> realize this is a strange question given that the
Hi Boaz,
I know that in some zinc-finger domains the zincs are coordinated by two
cysteins. The affinity of those is usually very high so they could be there
even if weren’t added in your buffers.
Cheers,
Lior
---
Lior Almagor, PhD
Weis Lab
Department of Structural Biology
Stanford
Dear all,
Carbohydrate molecules present in more than 14,000 PDB structures were
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Congratulations to the wwPDB biocurator Dr. Brian Hudson on processing
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Another possibility to model is a couple of S-hydroxy cysteines. We've seen
that in a Cys-amidase where there was artifactual oxidation damage to the
protein during storage or RT crystallization.
Roger Rowlett
On Wed, Dec 22, 2021, 8:00 AM Andrew Purkiss
wrote:
> As you say, the Cys are too
As you say, the Cys are too far apart for it to be a disulphide and it
looks like oxidation of the Cys. This could be due to radiation
damage, but other causes are possible.
A former colleague had one in betaB1-crystallin, which is visible in
pdbcode 1OKI at position 38. The difference density
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For anyone
Hi oliver,
Thanks! Real space refinment was done in phenix with default settings. The
position of these cysteines is quite constrained by where the main chain goes
and the Phe you can see just next to the cysteine. To me it seems it would
require very odd geometry to pull them into these
Could it not just be classical radiation damage, that is known to love
breaking SS bonds? If I understood correctly, single-particle cryo-EM
inflicts much higher radiation doses than X-ray crystallography.
Best wishes,
Gerard.
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On Wed, Dec 22, 2021 at 09:51:59AM +, Weiergräber, Oliver H.
