Hi Kavya
A few things I would try:
-set up your plates (and incubate) at 4 degrees - perhaps in a cold room
-use Alphafold model to identify patches of charge that you can mutate
-perhaps even introduce a few sticky motifs (e.g. herein and ref 26
Dear CCP4 list,
I have just tried accessing the "old" EBI PDBeMotif link and it is
non-functional. Assuming that it may or may not be moved/unavailable, I am
asking what your favourite methods are for mapping similar residue interactions
in dissimilar folds
i.e. if you have a nice network of
Dear ccp4 community,
When I see the (improving) accuracy of docking in generating drug like leads, I
see predominantly synthetic compounds used.
It occurred to me that it might be informative to use docking of naturally
occurring compounds (amino acids, sugars, lipids, factors etc) to find
Hi Scott
We have obtained a structure of a flexible clamshell like fold only after using
a disulphide mutant to lock the domains based on a Rosetta Fold model.
Interestingly, Alphafold put the very same residues further apart (probably a
relevant "open" pose)
Andy
Dear Board,
Perhaps off-topic, but in the wider scope it's relevant to many on here.
We have a gene that we are able to clone, and propagate in DH5a etc
non-expression cells (hence nucleotide sequence is non-toxic)
But, when we attempt to transfer to an expression strain we get no colonies
We
Dear All
Does anyone have a recommendation for a joint light/UV microscope for manual
Crystal screen inspection (i.e. a stand alone, not linked to automatation etc)?
Positive (ccp4bb) and negative (direct) impressions welcome!
Thanks
Andy
Dear All
just to clarify, I'd be most interested in examples resulting from proteolysis,
rather than say, packing effects
Best
Andy
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Dear CCP4bb,
I have a partly specific question, relating to multidomain enzymes.
We have a nice hi-res structure of an enzyme, which comprises domain A
(non-catalytic) and domain B (enzymatic)
Through the magic of unstimulated in-tray proteolysis, there are one and a half
copies in the ASU,
Dear CCP4ers
We have a protein with moderate resolution (mid 2s) with obvious metal ion
density holding the oligomer together. We can make an educated guess that the
ions are likely to be Mg/Ca and can look at co-ordination and bond
lengths.but I have a more specific question - would it be
To follow on from this thread:
To answer Jon, I did try to see if P6 subgroups were a possibility but can rule
this out for a few reasons (MR doesn't give solutions, merging stats not
suggestive of P6, the other dataset with the twin fraction that is
significantly further from 50:50); and the
Dear all,
I've a project with two historical datasets (i.e. not sure of when/if I can
reproduce to solve problem by getting better data) that are twinned.
The spacegroup is P32, with operator -h, -k, l
cell = 83.5 83.5 64.2 90 90 120
protein has three domains d1-d2-d3, likely 50% solvent,
Dear All
Many thanks to Johann for the suggestion of Topsearch - rather pleasingly our
tetramer is novel in the tetrameric arrangement, but each of the dimers has its
DNA recognition helices in agreement with several hits a win all round
Bringing joy to my lockdown.
Best
Andy
Thanks to all of you pointing me towards ProtCID, but unless I'm mistaken this
works only for deposited co-ordinates / PDB entries?
I was more looking for something that would take my (yet to be deposited) PDB
file, with its inherent tetrametric hth fold, and find similar folds in similar
Thanks Boaz for the SSM heads up. I was much too DALI-centric!
One last point, if anyone can offer an opinion - I presume most methods will
match but only within ASU contents.
Does any approach utilize deposited "biological unit" classification or (better
still) crystallographic symmetry
Dear colleagues,
I have a structure of a simple, common fold (hth, dna-binding) that I believe
has oligomerized in a different way to that observed for any members of the
superfamily that I can reasonably analyze.
So if I run fold comparison analysis (e.g. DALI) it will find similar
Hi Nikolas
The first thing I would try is to solubilise the protein a bit more, maybe by
adding a few % (1-5%) glycerol or ethylene glycol to the growth conditions when
you set up the drops.
The next thing would be to experiment with ratio (protein:precipitant) and drop
size.
Lastly, trial
Dear ccp4bb members,
A quick off topic question. I have a protein whose domain structure runs
N-TM-receptor-TM-enzyme-C, i.e. is a two transmembrane-helix containing
signalling protein. One would suspect that the receptor domain has ends that
cluster, and that the enzyme (via homology with
Dear all,
Thanks to Vincent, Eleanor, herman and others! It turns out I've managed to
sort it out a different way - the initial TFZ of 10 with cutout density and
resultant map was a bit underwhelming and indicative of an issue - so I cut my
~140ang long molecule in half and searched with
Ok - small oversight - I can see now that phenix has the atoms placed/saved
during cutout stage - so how best to use PHASER output to shift this file?
Andy
From: Andrew Lovering (School of Biosciences)
Sent: 10 January 2019 10:48
To: 'ccp4bb@jiscmail.ac.uk'
Subject: RE: complex multi-crystal
1 to match placed
density of MR in xtal2" :)
Andy
From: Andrew Lovering (School of Biosciences)
Sent: 09 January 2019 16:08
To: 'ccp4bb@jiscmail.ac.uk'
Subject: complex multi-crystal averaging
Dear All,
I suspect the way out of this is a new crystal (!) but interested to hear any
advice
Dear All,
A Wellcome-Trust postdoctoral position (for 2 years, possibly extendible to 4)
is open in the Lovering laboratory, using x-ray crystallography to study the
means by which predatory bacteria can form a pore in the prey outer membrane.
The link for the position is
Dear Jorge
This may not be exactly what you require, but there is a nice example of
analysis in the shift of a coiled coil register herein:
Elife. 2018 Jun 5;7. pii: e34815. doi: 10.7554/eLife.34815.
Asymmetric activation mechanism of a homodimeric red light-regulated
photoreceptor.
Best,
Andy
Dear All,
I have a protein from which I'd like to lose the co-purifying ligand (Coenzyme
A). The protein is his-tagged. The plan here is to bind it to a resin and then
run over a mild denaturant solution to encourage ligand loss (it seems that
extended dialysis does not achieve this).
Our
The backbone angle search in pdbemotif should limit it to particular secondary
structure.
Good luck!
Andy
From: xiaolei...@gmail.com [xiaolei...@gmail.com]
Sent: October 26, 2017 5:53 PM
To: Andrew Lovering; Joana Pereira
Cc: CCP4BB@JISCMAIL.AC.UK
Subject
I would guess that you want to search PDB for a small motif you've observed in
a structure of yours, looking to find examples of it used in same context?
If that's true, I would recommend PDBemotif, put the sequence in, and then use
the backbone psi phi angles of your motif as a secondary
]
Sent: 19 December 2016 19:58
To: Andrew Lovering
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] unusual monoclinic relation?
Dear Andrew,
did you remove all cysteins, and all methionines with the mutations? Your
resolution is about 2A, if I understand correctly. This may be suitable for S
for 2017! p.s. no anomalous signal in there - ironically mutant
we're using knocks bound metal out!
Thanks again
Andy
From: herman.schreu...@sanofi.com [mailto:herman.schreu...@sanofi.com]
Sent: 19 December 2016 16:26
To: Andrew Lovering; CCP4BB@JISCMAIL.AC.UK
Subject: AW: unusual monoclinic relation
and so I killed the job
thinking it was thrashing
Andy
From: herman.schreu...@sanofi.com [mailto:herman.schreu...@sanofi.com]
Sent: 19 December 2016 10:43
To: Andrew Lovering; CCP4BB@JISCMAIL.AC.UK
Subject: AW: unusual monoclinic relation?
Dear Andrew,
Just a few questions:
-Do the processing
Dear All,
I have just collected data on a mutant of a protein that should be facile to
solve by molrep (one residue/320 changed, approx 2Ang resolution) but is
proving problematic. Data merging stats look good.
The spacegroup is monoclinic, P21, the cell:
a=39.47 b=157.36 c=74.9 beta=98.26
I
(posted on behalf of Dr Anne-Marie Krachler)
Dear Colleagues,
Description for a postdoctoral position in the lab of Dr Anne-Marie Krachler,
University of Birmingham, UK;
Post is available from 1 March 2014
Postdoctoral Research Fellow (Structural Biology)
Applications are invited for a highly
Dear Colleagues,
Description for a postdoctoral position in the lab of Andrew Lovering,
University of Birmingham, UK; work following on from our recent publication in
Plos Pathogens:
http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002524
Funded by the BBSRC
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