Dear All,
I got the each of 6 mates coordination for each pdb by Coot or by Chimera. Then
viewed the arrangement of the 6 mates for 2zan or 2zao by Pymol or by Chimera.
You will find, for the 6 mates of 2zan, they were separated, but for 2zao they
were connected.
Then by pymol I align 2zan onto
Dear All,
I have a symmetry problem, which I hope I can get your help.
For both PDB 2zan and 2zam, they are for the same protein, they conformation
were similar except that 2zam was apo and 2zam was ATP binding. 2zaz was got by
soaking the 2zam crystal with ATP. Both were P65 space group
Howeve
Dear Colleagues,
We are pleased to announce the 10th annual CCP4 crystallographic school “>From
data collection to structure refinement and beyond”, held at Advanced Photon
Source (APS), Argonne National Laboratory (ANL). All details can be found at
http://www.ccp4.ac.uk/schools/APS-2017/index.
The main issue is that carboxyls seem to be invisible and Coot tries to fit
them as though the map had them there
Well, if the atoms are part of the model, then Coot will try to fit them to
the "data." I routinely chop off GLU and ASP side-chain when modelling into
cryo-EM maps (that's what th
Hello Eleanor,
We found some intermolecular vicinal disulfides recently that we think are
'real'. This class of proteins forms tetramers and in one version we find these
intermolecular disulfides across molecules. We did some tests and found that
oxidation or reduction has an effect on the sta
On 01/02/2017 17:11, Trevor Sewell wrote:
I have a 3.4 A (enzyme – protein only) map that I have fitted manually using
Coot and
automatically with Rapper. It all looks very nice – I can fit all but 13 of the
330
residues. I have the following questions:
Is there a way of having Coot know tha
Does this count as an example?
grep SSBOND /a/pdb/pdb4e9m.ent
SSBOND 1 CYS A 39CYS B 39 1555 1555 2.05
SSBOND 2 CYS C 39CYS D 39 1555 1555 2.04
SSBOND 3 CYS E 39CYS F 39 1555 1555 2.03
Dear Trevor,
I do not know if you are aware of it but there is a different version of refmac
which is just made for Cryo-EM refinements.
(http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/software.html)
In there, Refmac reports an average FSC value which is way more useful than the
R-facto
I have a 3.4 A (enzyme – protein only) map that I have fitted manually using
Coot and automatically with Rapper. It all looks very nice – I can fit all but
13 of the 330 residues. I have the following questions:
Does refmac5 have a way of refining the scale of the map? – I did my best to
calibr
Dear all,
thanks for your
input
cheers!!
G.
On 1 Feb 2017, at 17:17, Debanu
mailto:debanu@gmail.com>> wrote:
Dear Xavier,
Great point and reminder!
Thanks,
Debanu
On Feb 1, 2017, at 6:44 AM, Boaz Shaanan
mailto:bshaa...@bgu.ac.il>> wrote:
Hi,
One possible (formal, I should say) wa
Thank you for all this information, and especially Paul for having a good
search query - I had got nothing useful from any I tried at PDBe or RSCB.
No idea why it has been formed - the fold is identical to a high resolution
example (1.3A) where the disulphide links the N & C termini within a
sing
Dear Xavier,
Great point and reminder!
Thanks,
Debanu
> On Feb 1, 2017, at 6:44 AM, Boaz Shaanan wrote:
>
> Hi,
> One possible (formal, I should say) way around this would be to use one of
> the homology modeling servers (my favourite recently is phyre2 but go for any
> server you prefer) and
Oh dear - more symmetry Qs.
This has arisen from the SSBOND to a symmetry equivalent puzzle with
links 1_555 (X,Y,Z) to 9_565 (X,1+X-y,1/6-Z) IF you are using the $CLIB/
symlib.info
but links 1_555 to 12_565 if you are using the mmdb order of symmetry
operators..
.
Aaaah!!!
Eleanor
Dear Eleanor,
I did not check the pdb file you mentioned, but I have had a case like that.
The protein formed a complex of 8 large and 8 small subunits with internal 422
symmetry. There was a disulfide link across the internal twofolds and in one of
the crystal forms we got, this internal twofo
I solved a structure years ago (1L31 and a couple related entries) which had
intermolecular oligomerizing disulfides in some of the crystals (reciprocal
C23-C27’ and C23’-C27). I thought at the time that they seemed too “deliberate”
to be just an artifact, but others thought that since the enzym
Hi Sundaram,
The binding capacity of this column is 40 mg/mL of resin so a 5mL column
will hold a maximum of 200 mg of protein. If you run your cleared lysate
on a gel you may be able to estimate how much protein there is. Our
facility purifies a range of different proteins for investigators and
Does anyone know of examples of these?
I have found one - 2WQW with these SSBOND records
2WQW
SSBOND 1 CYS A 206CYS A 227 1555 6556
2.07
SSBOND 2 CYS B 206CYS B 227 1555 5556
2.15
We seem to have one but it would have to form af
Hi,
One possible (formal, I should say) way around this would be to use one of the homology modeling servers (my favourite recently is phyre2 but go for any server you prefer) and feed it with the sequence of the protein in your structure as if you're trying
to get its structure in the''apo''
CNS, if sequences are identical.
Sent from Jack's iPhone
> On Feb 1, 2017, at 4:26 AM, Madhuranayaki Thulasingam
> wrote:
>
> Dear all,
>
> I would like to plot RMSD vs amino acids for two superimposed crystal
> structures.
>
> Can anyone suggest me a way to do it.
>
> Thanks in advance,
Dear Madhu
I think LSQKAB does what you want
http://www.ccp4.ac.uk/html/lsqkab.html
(at least, from the description you gave)
Best wishes Graeme
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Madhuranayaki Thulasingam
Sent: 01 February 2017 10:25
To: ccp4bb
Subject: [cc
Dear all,
I would like to plot RMSD vs amino acids for two superimposed crystal
structures.
Can anyone suggest me a way to do it.
Thanks in advance,
Madhu.
Dear Sundaram S,
during my PhD I used 4-7.5ml resin per l of culture, but I also had a large
yield of 60-100mg protein per litre. Try to use as little as possible - at
first trial check both flow-through and retentate by SDS-PAGE. (see. p. 40 and
54 of my thesis).
My constructs would also bind
This should give you everything you need to know about the column
http://www.sigmaaldrich.com/technical-documents/protocols/biology/roche/complete-his-tag-purification-column.html
I'd definitely say load all of your lysate, possibly run it through twice if
you really want to. If you're worried
Hello ,
It's an off topic question.
I'm planning to do manual purification a 6 his tagged protein of size
around 20kDa from 1L E.coli culture using
COHISC-RO Roche cOmplete™ His-Tag Purification Column.
Can I get some advice regarding the lysate loading volume and retention
time.
This is the fi
Dear all,
just a side comment to Guillermo's and Debanu´s discussion, which deals
with the term "apo".
I got the text below from a reviewer, who—as an exception ;-)—was
absolutely right:
In enzymology, enzymes that require the aid of cofactors such as metal
ions or prosthetic groups (e.g.
Hi,
indeed, very difficult nowadays to get your hands on a monitor with
build-in IR-emitter in order to avoid needing to buy an expensive Nvidia
card with a 3-pin connector.
On the other hand, on EBAY many older Nvidia cards are being offered
that have a 3-pin connector and that are fast eno
26 matches
Mail list logo
