[ccp4bb] postdoc 3

[IGOR VALENCIA]

Los últimos 2 (numero 2 y 3 en el asunto, tienen una oferta de estudio de 
flagelos = flagella)

Saludos

De: CCP4 bulletin board  en nombre de CCP4BB automatic 
digest system 
Enviado: martes, 19 de abril de 2016 06:00 p. m.
Para: CCP4BB@JISCMAIL.AC.UK
Asunto: CCP4BB Digest - 18 Apr 2016 to 19 Apr 2016 (#2016-112)

There are 15 messages totaling 2009 lines in this issue.

Topics of the day:

  1. measuring the angle (2)
  2. Fwd: Postdoc position available in Prof. Patti LiWang's lab at University
 of California, Merced
  3. Unusual diffraction (2)
  4. PhaseMR - Twinning? (2)
  5. FW: Postdoc opportunity at University of Texas, Austin
  6. Releases of new stable versions of Global Phasing software
  7. Co-crystallization with glycerophosphocholine (2)
  8. X-ray Crystallography/Drug Discovery Postdoctoral Position at the
 University of Georgia
  9. Vacancy for a scientific data curator (PDB/EMDB) at PDBe
 10. Switching projects broken?
 11. Equipment and software for protein crystallization imaging and
 optimization

--

Date:Tue, 19 Apr 2016 02:23:34 +
From:Sagar Khavnekar 
Subject: Re: measuring the angle

Dear Chemocev,

You can possibly do it with python.

Check this link.
https://sourceforge.net/p/pymol/mailman/message/33229437/

Else, superpose proteins for the center of mass of each subunit. Calculate
angle using rotation matrix.

I am not sure if you can superpose protein molecules so that their center
of mass coincide. Or else just superpose with lsq.

Cheers,

Sagar

On Tue 19 Apr, 2016 2:20 am chemocev marker,  wrote:

> Hi All
> I am trying to understand some protein structures and want to know how I
> can measure the angle between two subunits of heterodimer molecules.
>
> best
>
> Jiri
>

--

Date:Tue, 19 Apr 2016 02:28:11 +
From:Sagar Khavnekar 
Subject: Re: measuring the angle

Or else just use dyndom.
http://fizz.cmp.uea.ac.uk/dyndom/
DynDom - Protein Domain Motion
fizz.cmp.uea.ac.uk
DynDom is a program to determine domains, hinge axes and hinge bending residues 
in proteins where two conformations are available





On Tue 19 Apr, 2016 7:53 am Sagar Khavnekar, 
wrote:

> Dear Chemocev,
>
> You can possibly do it with python.
>
> Check this link.
> https://sourceforge.net/p/pymol/mailman/message/33229437/
>
> Else, superpose proteins for the center of mass of each subunit. Calculate
> angle using rotation matrix.
>
> I am not sure if you can superpose protein molecules so that their center
> of mass coincide. Or else just superpose with lsq.
>
> Cheers,
>
> Sagar
>
> On Tue 19 Apr, 2016 2:20 am chemocev marker,  wrote:
>
>> Hi All
>> I am trying to understand some protein structures and want to know how I
>> can measure the angle between two subunits of heterodimer molecules.
>>
>> best
>>
>> Jiri
>>
>

--

Date:Mon, 18 Apr 2016 23:16:17 -0400
From:Steve Chou 
Subject: Fwd: Postdoc position available in Prof. Patti LiWang's lab at 
University of California, Merced

Dear CCP4BB subscribers,

I'm posting this ad on behalf of Prof. Patti LiWang. A postdoc position is
open in her lab at University of California, Merced. See the info below for
details. The position represents an excellent opportunity for researchers
to develop their careers. Interested and qualified individuals can apply
through the following official link.
All the best,
Steve




https://aprecruit.ucmerced.edu/apply/JPF00346



*Open date: *April 18th, 2016
*Next review date: *May 18th, 2016
Apply by this date to ensure full consideration by the committee.
*Final date: *May 18th, 2016
Applications will continue to be accepted until this date, but those
received after the review date will only be considered if the position has
not yet been filled.
DESCRIPTION

A Postdoctoral Scholar position is available in the biochemical and
biophysical research lab at the University of California, Merced. This
position primarily involves carrying out biochemical research on proteins
to study inflammation and HIV inhibition. This work will include protein
expression and purification from multiple sources such as E. coli, yeast,
and mammalian cells; Molecular biology such mutagenesis and ELISA assays;
Mammalian cell culture and biological assays including binding and
single-round virus infectivity assays. Research may also include
biophysical techniques such as NMR, 

Re: [ccp4bb] Refmac5 update water option

[Xiao Lei]

Got it. Thank you very much Christian!

On Fri, Dec 16, 2016 at 12:14 PM, Christian Roth  wrote:

> Hi,
>
> the adding water option is basically a COOT script to find waters, which
> get subsequently refined. There is no automatic evaluation and deletion of
> waters based on certain criteria. That you have to do manually. You can
> always try to automatically add new waters, which is done by this option in
> later refinement runs of course, but that doesn't "touch" the waters
> previously added to the model.
>
> Cheers
>
> Christian
>
> Am 16.12.2016 um 19:50 schrieb Xiao Lei:
>
> Dear CCP4bb members,
>
> Does Refmac5 in CCP4i have an option of adding waters to the refined
> structure (the input coordinate does not have any water)?  I see in Phenix
> refine there is an option of "update water", I tried to look for this
> option in Refmac5 but I could not find it. I am using CCP4i 7.0.025 version.
>
>
>

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

[Alex Lee]

Dear All,

I really appreciate your nice explanations!



On Fri, Dec 16, 2016 at 12:08 PM, Eleanor Dodson 
wrote:

>
> This isnt the sort of thing a refinement program does.
> Refinement starts from the model you provide - uses that to generate
> phases and the appropriately weighted difference map to alter the input
> coordinates.
> So that map is used in the close environment of a the model, so solvent
> flattening is not an important option. ( There is an element of these in
> the choice of scale between Fobs and Fcalc but it isnt explicit. ]
>
> NCS averaging is useful, but it is done by imposing NCS on the refined
> models.
>
>
> However if you want to do automated rebuilding using BUCCANEER or Arp/Warp
> it may be worth first generating phases by a good many cycles of REFMAC,
> then using PARROT to impose ncs symmetry and solvent flattening, then
> beginning the rebuild cycles with these phases.
>
> This approach is provided in CCP4I2
> Eleanor
>
> On 16 December 2016 at 19:44, Alex Lee  wrote:
>
>> Hi All,
>>
>> I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5
>> automatically does density modification (e.g. solvent flattening, NCS,
>> etc..) in the refinement after I put a solution coordinate from Phaser MR
>> molecular replacement and the experiment data (MTZ file)?   If Refmac5 does
>> not do density modification automatically, is it better that first doing a
>> density modification (CCP4i DM or Pirate) after molecular replacement
>> (input the solution coordinate file and mtz map generated by Phaser MR),
>> and then building structures and finally do the Refmac5?
>>
>>
>>
>

Re: [ccp4bb] Refmac5 update water option

[Christian Roth]

Hi,

the adding water option is basically a COOT script to find waters, which 
get subsequently refined. There is no automatic evaluation and deletion 
of waters based on certain criteria. That you have to do manually. You 
can always try to automatically add new waters, which is done by this 
option in later refinement runs of course, but that doesn't "touch" the 
waters previously added to the model.


Cheers

Christian


Am 16.12.2016 um 19:50 schrieb Xiao Lei:

Dear CCP4bb members,

Does Refmac5 in CCP4i have an option of adding waters to the refined 
structure (the input coordinate does not have any water)?  I see in 
Phenix refine there is an option of "update water", I tried to look 
for this option in Refmac5 but I could not find it. I am using CCP4i 
7.0.025 version.

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

[Artem Evdokimov]

DM will be most helpful to you if you are as unbiased as possible to begin
with. I *think* that DM right after MR is about as biased as DM after MR
after a round of Refmac post-MR (given that MR these days includes rigid
body refinement anyway) but I would be very curious to hear what the
resident theoreticians have to say about this, in terms of actual
mathematics.

The maximum benefit you can get from DM will come through if you also
include NCS averaging (if you have NCS of course). Nowadays you can try a
number of nice DM routines - and don't forget Resolve - each offering
somewhat unique advantages. You should also carefully estimate actual
solvent content, and other pre-set parameters since they will have
considerable effect on the quality and meaningfulness (unbiased information
content?) of the resulting maps.

Incidentally, it is always good to have a few practical indicators of bias
removal e.g. to delete a residue in a search model and then see it come
back in post-DM maps or to observe difference density near parts of the
search model that differ in the actual structure.

Artem
www.harkerbio.com
"Speed of a cheetah, strength of a bear and tenacity of a divorce lawyer"

On Fri, Dec 16, 2016 at 2:44 PM, Alex Lee  wrote:

> Hi All,
>
> I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5
> automatically does density modification (e.g. solvent flattening, NCS,
> etc..) in the refinement after I put a solution coordinate from Phaser MR
> molecular replacement and the experiment data (MTZ file)?   If Refmac5 does
> not do density modification automatically, is it better that first doing a
> density modification (CCP4i DM or Pirate) after molecular replacement
> (input the solution coordinate file and mtz map generated by Phaser MR),
> and then building structures and finally do the Refmac5?
>
>
>

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

[Christian Roth]

Dear Alex,

Refmac doesn't do density modification. If you want take advantage of 
better starting phases you have to do DM prior Refmac or model building 
with Buccaneer for example. I recommend PARROT for that.
I would use i2 Parrot and this as input in the Buccaneer pipeline with 
precomputed phases form Parrot.



Cheers

Christian

Am 16.12.2016 um 19:44 schrieb Alex Lee:

Hi All,

I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5 
automatically does density modification (e.g. solvent flattening, NCS, 
etc..) in the refinement after I put a solution coordinate from Phaser 
MR molecular replacement and the experiment data (MTZ file)?   If 
Refmac5 does not do density modification automatically, is it better 
that first doing a density modification (CCP4i DM or Pirate) after 
molecular replacement (input the solution coordinate file and mtz map 
generated by Phaser MR), and then building structures and finally do 
the Refmac5?

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

[Eleanor Dodson]

This isnt the sort of thing a refinement program does.
Refinement starts from the model you provide - uses that to generate phases
and the appropriately weighted difference map to alter the input
coordinates.
So that map is used in the close environment of a the model, so solvent
flattening is not an important option. ( There is an element of these in
the choice of scale between Fobs and Fcalc but it isnt explicit. ]

NCS averaging is useful, but it is done by imposing NCS on the refined
models.


However if you want to do automated rebuilding using BUCCANEER or Arp/Warp
it may be worth first generating phases by a good many cycles of REFMAC,
then using PARROT to impose ncs symmetry and solvent flattening, then
beginning the rebuild cycles with these phases.

This approach is provided in CCP4I2
Eleanor

On 16 December 2016 at 19:44, Alex Lee  wrote:

> Hi All,
>
> I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5
> automatically does density modification (e.g. solvent flattening, NCS,
> etc..) in the refinement after I put a solution coordinate from Phaser MR
> molecular replacement and the experiment data (MTZ file)?   If Refmac5 does
> not do density modification automatically, is it better that first doing a
> density modification (CCP4i DM or Pirate) after molecular replacement
> (input the solution coordinate file and mtz map generated by Phaser MR),
> and then building structures and finally do the Refmac5?
>
>
>

[ccp4bb] Refmac5 update water option

[Xiao Lei]

Dear CCP4bb members,

Does Refmac5 in CCP4i have an option of adding waters to the refined
structure (the input coordinate does not have any water)?  I see in Phenix
refine there is an option of "update water", I tried to look for this
option in Refmac5 but I could not find it. I am using CCP4i 7.0.025 version.

[ccp4bb] does Refmac5 do density modification in the refinement of a structure?

[Alex Lee]

Hi All,

I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5
automatically does density modification (e.g. solvent flattening, NCS,
etc..) in the refinement after I put a solution coordinate from Phaser MR
molecular replacement and the experiment data (MTZ file)?   If Refmac5 does
not do density modification automatically, is it better that first doing a
density modification (CCP4i DM or Pirate) after molecular replacement
(input the solution coordinate file and mtz map generated by Phaser MR),
and then building structures and finally do the Refmac5?

Re: [ccp4bb] jligand help

[Robbie Joosten]

Hi Nicholas,

CCP4 6.5 is end-of-life and no longer supported. Please upgrade to version 7.0. 
Apart from the obvious benefit of having up-to-date softeare, JLigand should 
also work.

Cheers,
Robbie

Sent from my Windows 10 phone

Van: Nicholas Larsen
Verzonden: vrijdag 16 december 2016 18:35
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] jligand help

Dear All,
I have CCP4 6.5.0 installed on my laptop PC.  Everything runs fine, to my 
knowledge, except JLigand.  When I click this program from the program list, 
absolutely nothing happens.  No error message, nothing.  It doesn't launch.  Do 
I need to reinstall cpp4 or is JLigand a separate installation?

Thanks for any suggestion,
Nick

[This e-mail message may contain privileged, confidential and/or proprietary 
information of H3 Biomedicine. If you believe that it has been sent to you in 
error, please contact the sender immediately and delete the message including 
any attachments, without copying, using, or distributing any of the information 
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any legally-binding agreement or contract.]

[ccp4bb] jligand help

[Nicholas Larsen]

Dear All,
I have CCP4 6.5.0 installed on my laptop PC.  Everything runs fine, to my
knowledge, except JLigand.  When I click this program from the program
list, absolutely nothing happens.  No error message, nothing.  It doesn't
launch.  Do I need to reinstall cpp4 or is JLigand a separate installation?

Thanks for any suggestion,
Nick

-- 
[This e-mail message may contain privileged, confidential and/or 
proprietary information of H3 Biomedicine. If you believe that it has been 
sent to you in error, please contact the sender immediately and delete the 
message including any attachments, without copying, using, or distributing 
any of the information contained therein. This e-mail message should not be 
interpreted to include a digital or electronic signature that can be used 
to authenticate an agreement, contract or other legal document, nor to 
reflect an intention to be bound to any legally-binding agreement or 
contract.]

Re: [ccp4bb] Averaging of different proteins in heteromeric complex

[David Schuller]

"The proteins are stoichiometric"

Huh? What is the stoichiometry? I'm expecting a ratio here, like 1:1 or 
some such.


I see two possibilities:

1) The two proteins are completely interchangeable in the structure.

2) The two proteins are not interchangeable, but are being 
crystallographically averaged.


To differentiate, I would want more info, not necessarily crystallographic.

Do pure samples of either protein form the same structure (double hex ring)?

Does the stoichiometry of the complex ever vary?

Is there any data to suggest that the complex behaves any differently 
than pure samples of either protein?


Do you have any non-crystallographic data on complex formation - 
cross-linking results, etc. ?


On 12/16/16 11:45, Graham Robinson wrote:


Dear Crystallographers,

I have solved the structure of a complex, which is the average of its 
component proteins. The problem is as follows:


The complex is composed of two proteins, which share 67%/84% sequence 
identity/similarity in the resolvable region. The proteins are 
stoichiometric (SDS-PAGE of the crystals), and form a dodecamer 
composed of two hexameric rings, stacked on top of one another.


The crystals are H3. Analysis with Xtriage, Pointless, Aimless, Scala 
do not find other space groups likely, and do not find any apparent 
data pathologies. Data processing in H3 (to 1.9 A) is straight forward 
(Rfactor/Rfree: 22.3%/26.4% using one of the proteins as MR model). 
Attempts to solve the structure in other space groups (except P1) 
fail, or produce meaninglessly poor statistics.


I have good anomalous data from isomorphous SeMet crystals, and the 
anomalous difference density peaks for the Se are approximately 
additive: anomalous peaks for positions where SeMet is unique to one 
of the two proteins are about 1/2 the size of peaks common to both 
proteins. This composite effect is apparent when the structure is 
processed in P1 also.


Crystal contacts are not specific to either of the two proteins, and 
so it appears that the crystal doesn't distinguish between up- and 
down-orientations of the dodecameric rings. Therefore, each subunit in 
the resulting structure is a composite of the two proteins.


Despite the occurrence of heteromeric rings in protein structures, I 
have not been able to find a description of this problem in the 
literature, nor the archives of the CCP4BB.


I am keen to hear from anyone who has observed similar things in 
structures of their complexes, and how best to approach this problem.


Many thanks,

Graham Robinson

Postdoc, University of Geneva

Graham Robinson, Ph.D.

Fitzpatrick Group

Département de Botanique et Biologie Végétale

Université de Genève

30 Quai Ernest-Ansermet

CH-1211, Genève 4

T: +41 (0) 22/379.30.12




--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] Averaging of different proteins in heteromeric complex

[Keller, Jacob]

This seems like a case of what is called either static or statistical disorder. 
Axel Brunger has a JMB paper about this with DNA crystals:
http://atbweb.stanford.edu/scripts/papers.php?sendfile=30
JPK


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graham 
Robinson
Sent: Friday, December 16, 2016 11:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Averaging of different proteins in heteromeric complex

Dear Crystallographers,
I have solved the structure of a complex, which is the average of its component 
proteins. The problem is as follows:
The complex is composed of two proteins, which share 67%/84% sequence 
identity/similarity in the resolvable region. The proteins are stoichiometric 
(SDS-PAGE of the crystals), and form a dodecamer composed of two hexameric 
rings, stacked on top of one another.
The crystals are H3. Analysis with Xtriage, Pointless, Aimless, Scala do not 
find other space groups likely, and do not find any apparent data pathologies. 
Data processing in H3 (to 1.9 A) is straight forward (Rfactor/Rfree: 
22.3%/26.4% using one of the proteins as MR model). Attempts to solve the 
structure in other space groups (except P1) fail, or produce meaninglessly poor 
statistics.
I have good anomalous data from isomorphous SeMet crystals, and the anomalous 
difference density peaks for the Se are approximately additive: anomalous peaks 
for positions where SeMet is unique to one of the two proteins are about 1/2 
the size of peaks common to both proteins. This composite effect is apparent 
when the structure is processed in P1 also.
Crystal contacts are not specific to either of the two proteins, and so it 
appears that the crystal doesn't distinguish between up- and down-orientations 
of the dodecameric rings. Therefore, each subunit in the resulting structure is 
a composite of the two proteins.
Despite the occurrence of heteromeric rings in protein structures, I have not 
been able to find a description of this problem in the literature, nor the 
archives of the CCP4BB.
I am keen to hear from anyone who has observed similar things in structures of 
their complexes, and how best to approach this problem.
Many thanks,
Graham Robinson
Postdoc, University of Geneva

Graham Robinson, Ph.D.
Fitzpatrick Group
Département de Botanique et Biologie Végétale
Université de Genève
30 Quai Ernest-Ansermet
CH-1211, Genève 4
T: +41 (0) 22/379.30.12

[ccp4bb] Averaging of different proteins in heteromeric complex

[Graham Robinson]

Dear Crystallographers,
I have solved the structure of a complex, which is the average of its component 
proteins. The problem is as follows:
The complex is composed of two proteins, which share 67%/84% sequence 
identity/similarity in the resolvable region. The proteins are stoichiometric 
(SDS-PAGE of the crystals), and form a dodecamer composed of two hexameric 
rings, stacked on top of one another.
The crystals are H3. Analysis with Xtriage, Pointless, Aimless, Scala do not 
find other space groups likely, and do not find any apparent data pathologies. 
Data processing in H3 (to 1.9 A) is straight forward (Rfactor/Rfree: 
22.3%/26.4% using one of the proteins as MR model). Attempts to solve the 
structure in other space groups (except P1) fail, or produce meaninglessly poor 
statistics.
I have good anomalous data from isomorphous SeMet crystals, and the anomalous 
difference density peaks for the Se are approximately additive: anomalous peaks 
for positions where SeMet is unique to one of the two proteins are about 1/2 
the size of peaks common to both proteins. This composite effect is apparent 
when the structure is processed in P1 also.
Crystal contacts are not specific to either of the two proteins, and so it 
appears that the crystal doesn't distinguish between up- and down-orientations 
of the dodecameric rings. Therefore, each subunit in the resulting structure is 
a composite of the two proteins.
Despite the occurrence of heteromeric rings in protein structures, I have not 
been able to find a description of this problem in the literature, nor the 
archives of the CCP4BB.
I am keen to hear from anyone who has observed similar things in structures of 
their complexes, and how best to approach this problem.
Many thanks,
Graham Robinson
Postdoc, University of Geneva

Graham Robinson, Ph.D.
Fitzpatrick Group
Département de Botanique et Biologie Végétale
Université de Genève
30 Quai Ernest-Ansermet
CH-1211, Genève 4
T: +41 (0) 22/379.30.12

[ccp4bb] NIH-funded postdoc position

[Deaconescu, Alexandra]

Dear colleagues,

Please see below an ad for an NIH-funded postdoc position in my laboratory.

Thank you,
Alexandra


*POSTDOCTORAL POSITION*
*at Brown University, Providence, Rhode Island, USA*

The Deaconescu Lab at Brown University is seeking a motivated and 
energetic postdoctoral research to join our work on a NIH-funded project.


Our work focuses on stress responses such as to DNA damage and 
starvation, and particularly on the interplay between transcription, DNA 
repair and chromatin remodeling. Our work so far has  elucidated the 
function and mechanochemistry of DNA-based motors and also of 
cytoskeletal regulators using a combination of biochemical, biophysical 
and structural techniques. (e.g. X-ray crystallography, small-angle 
X-ray scattering, transmission electron microscopy). For recent examples 
of work, please see Deaconescu and Suhanovsky, Photochem and 
Photobiology (2016), Kutter et al. JMB (2016), Szyk et al., Cell (2014), 
Deaconescu et al., PNAS (2012), Szyk et al., NSMB (2012) and Deaconescu 
et al., TIBS (2013).


Brown University has a Structural Biology Core Facility managed by a 
PhD-level scientist and features, among others, an X-ray generator 
equipped with an ACTOR mounting robot as well as 500 and 850 MHz NMR 
magnets.


A successful candidate should have the following qualifications: a Ph.D. 
in the field of Molecular Biology, Cell Biology, Biochemistry or related 
field; an established track-record of publications in peer-reviewed 
journals; solid experience in the biochemistry of complex DNA-binding 
proteins, their purification from E.coli/yeast expression systems as 
well as their characterization using functional studies such as by 
isothermal titration calorimetry, transcription assays, circular 
dichroism and fluorescence.  Prior knowledge of crystallography would be 
a plus, but is not required. Must be highly motivated and work 
independently as well as in a team. Excellent spoken and written English 
are required. New Ph.D. graduates are encouraged to apply. Salary and 
starting date are negotiable.


Interested candidates should send a CV, one page research experience 
summary and contact information for three references to 
alexandra_deaconescu[at]brown.edu. Salary and starting date are 
negotiable. _Please write Postdoctoral Candidate in the e-mail subject 
header_.   Brown University, an Ivy League institution, is located less 
than one hour away by train from Boston.


Lab webpage:*https://deaconesculab.com*


--
Alexandra M. Deaconescu, B.E., Ph.D.
Assistant Professor of Molecular Biology, Cell Biology and Biochemistry
Brown University

For mail:
70 Ship St. G-E4
Providence, RI 02903

For courier (FEDEX):
70 Ship St.
Chestnut St. Loading Dock
Providence, RI 02903

Phone: 401-863-3215
Lab website: http://deaconesculab.com

Administrative Assistant: Mr. Ray Windsor (phone: 401-863-7446)

[ccp4bb] PhD opportunity in membrane protein structural biology (Leeds, UK)

[Maren Thomsen]

Dear all,

on behalf of a colleague I am posting a very interesting PhD position.
For further information please see
https://www.findaphd.com/search/ProjectDetails.aspx?PJID=81598=735  or
email s.harbo...@leeds.ac.uk.
Application deadline is the 31.01.2017.



*Structural characterisation of the human equilibrative nucleoside
transporter, a target for cancer, malaria and AIDS*
Our goal is to understand the structure and mechanism of equilibrative
nucleoside transporters (ENTs), a key family of membrane protein
transporters important in cancer, malaria and AIDS. Integral membrane
proteins comprise approximately 30% of the human proteome, representing a
significant target for drug discovery efforts. Despite this, we currently
have very little structural information about them: only ≈2% of the protein
structures solved to date represent novel membrane protein families, and
even fewer are eukaryotic proteins.

Primarily the focus of the project will be on the expression, purification,
stabilisation and structural characterisation of ENTs by X-ray
crystallography and cryo-EM. The project will allow training in a broad
range of structural and biochemical techniques applied to membrane
proteins; such as:
-insect and mammalian cell culture
-radioactive binding assays
-thermostability assays
-analytical size exclusion
-X-ray crystallography
-cryo-EM
-molecular dynamics simulations

ENTs represent an important class of protein for pharmacological treatment
of cancer (1), protozoan parasites such as Plasmodium falciparum (malaria)
(2) and viral diseases such as AIDS (3). Under physiological circumstances,
the ENTs are involved in the uptake of nucleosides and nucleobases into
cells, salvaging important building-blocks for the synthesis of DNA and RNA
(3). ENTs are ubiquitously expressed across human tissues (3), and their
function is particularly important in erythrocytes, leukocytes, bone marrow
cells and some cells in the brain, which are deficient for de-novo
synthesis of nucleotides (3). Furthermore, ENTs directly influence the
concentration of adenosine available to cell surface receptors (3) and so
processes such as coronary blood flow, myocardial O2 supply–demand balance,
inflammation and neurotransmission.

The project will be carried out in the Astbury Centre for Structural
Biology one of the most diverse, multidisciplinary structural biology
centres in the world. It encompasses 75 groups in Physics, Chemistry and
Biological Sciences. With a recent £17 million investment by the University
of Leeds and further investment by the Wellcome Trust and BBSRC in
structural molecular biology the project will have access to world leading
state of the art membrane protein production, X-ray crystallography and
cryo-EM facilities.

*Funding Notes*

Fully funded BBSRC iCASE studentship, providing UK/EU level fees plus a
stipend (£14,296) for 4 years. EU candidates must have resided in the UK
for three years prior to the start of the PhD to be eligible for full
support; without evidence of residency the studentship will only provide
fees and no stipend. Non-UK/EU candidates are not eligible. Candidates
should have or be expecting a 2.1 or above at undergraduate level in a
relevant subject. If English is not your first language you will be
required to meet our English language requirements. The start date will be
Oct 2017.

*References: *

1. T. Oguri et al., Cancer Lett. 256, 112–119 (2007).
2. R. Deniskin et al., Int. J. Parasitol. Drugs Drug Resist. 6, 1–11
(2016).
3. J. D. Young et al., Xenobiotica. 38, 995–1021 (2008).

[ccp4bb] CCP4 update 026

[Charles Ballard]

Dear All

contains updates to coot for linux 32/64-bit and OS X.  This re-corrects the 
auto-mutate problem on OS X, and various segv such as when using coot-mini-rsr.

Hopefully we now have a functional coot.  

Thank you for bearing with us

Charles on behalf of the CCP4 core team.

[ccp4bb] Call for access to Synchrotron Beamline Facilities, 2017 - EMBL Hamburg, Germany

[Sarah Marshall]

 

CALL FOR ACCESS TO SYNCHROTRON BEAMLINE FACILITIES, 2017 - EMBL HAMBURG, GERMANY

We announce a call for synchrotron beam time applications in biological 
small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX) for 
the period April - December 2017. The following EMBL beamlines at PETRA III 
(DESY, Hamburg) are available: P12 (SAXS), P13 (MX), and P14 (MX).

Single proposals and BAG proposals are now being accepted for both methods, MX 
and SAXS. Groups applying for beamtime to work on several projects are strongly 
encouraged to submit a BAG (Block Allocation Group) proposal. The deadline for 
submission of proposals is JANUARY 23RD, 2017, after which the proposals will 
be evaluated by an external Project Evaluation Committee. The users will be 
informed about the results of their application by March 13th, 2017.

A detailed description of the three beamlines and links to the electronic 
proposal forms can be found at:

SAXS: http://www.embl-hamburg.de/services/saxs/index.html[1]
MX: http://www.embl-hamburg.de/services/mx/index.html[2]

 Submit a proposal via the EMBL Hamburg user portal[3]

Access to the EMBL Hamburg facilities also includes assistance with 
crystallisation, sample preparation and, in combination with an EMBL beamline 
visit, with sample characterisation and optimisation. Usage of the beamlines 
and biophysical facilities for translational research can in part be supported 
by the iNEXT project (http://www.inext-eu.org/access/[4]), a Horizon 2020 
programme of the European Union.

For further general information, please contact the EMBL Hamburg user office:
Tel.: +49 40-89902-111 / 183
Email: useroffice (at) embl-hamburg.de

For specific information:
saxs (at) embl-hamburg.de (small-angle X-ray scattering)
mx (at) embl-hamburg.de (macromolecular crystallography)
spc (at) embl-hamburg.de (sample preparation and characterization) 

Links:
--
[1] http://www.embl-hamburg.de/services/saxs/index.html
[2] http://www.embl-hamburg.de/services/mx/index.html
[3] https://smis.embl-hamburg.de
[4] http://www.inext-eu.org/access/

Re: [ccp4bb] AW: Could this be a complex crystal? or only RNA crystal? or micromolecular？

[Camillo Rosano]

dear Rachel,
  to me this seems more like a salt diffraction
pattern... I agree with Kevin, run a SDS on your crystal and see if you
have crystallized something "interesting"
Good luck

On Fri, Dec 16, 2016 at 9:26 AM, Camillo Rosano 
wrote:

> dear Rachel,
>   to me this seems more like a salt diffraction
> pattern... I agree with Kevin, run a SDS on your crystal and see if you
> have crystallized something "interesting"
> Good luck
> Camillo
>
> On Fri, Dec 16, 2016 at 9:10 AM,  wrote:
>
>> Dear Rachel,
>>
>>
>>
>> You don’t have any spots with a resolution lower than ca. 15Å, which
>> means that none of the cell axes can be longer than 15Å. This must be a
>> crystal of some small molecule and not of a protein and/or RNA molecule.
>>
>>
>>
>> One question: you mention that the data could not be processed by
>> HKL2000; where did then the unit cell you quote come from? You could try
>> indexing your data with small-molecule settings, e.g. allowing a very small
>> unit cell.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Liu Rachel
>> *Gesendet:* Donnerstag, 15. Dezember 2016 18:54
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [ccp4bb] Could this be a complex crystal? or only RNA
>> crystal? or micromolecular？
>>
>>
>>
>>
>>
>> Dear everyone:
>>
>>
>>
>> Recently, I suffered a problem during my research work. I
>> co-purified a zinc finger protein(152aa) and a dsRNA(19bp), the
>> final SEC buffer is *20mM Hepes, 150mM NaCl, pH8.0*. Then the
>> complex was co-crystallized by vapor diffusion against a solution of *30% 
>> PEG400, 0.2M
>> MgCl, 0.1M Tris pH8.4. * The crystal is very beautiful, but the
>> X-ray diffraction diagram is very strange, the diffraction point looks
>> big and sparse(as shown in the picture). The Data cannot
>> be processed with HKL2000 either.
>>
>>  unit_cell = 24.808 42.863 119.042 90 90 90
>>
>>  space_group = "I 2 2 2"
>>
>>
>>
>> I wanna figure out, could this be a complex crystal? or only RNA
>> crystal? or other micromolecular?
>>
>>
>>
>> PS. I've set drops without the protein in the sample, but prepare
>> the sample of RNA with the protein buffer as if the protein was there. And
>> there was no crystallization .
>>
>>
>>
>> Thank you very much!
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Rachel Liu
>>
>> Room 2071, research center in life sciences,
>>
>> China Agricultural University
>>
>> No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  P.R. China
>>
>> Tel: (86)-10-62734078
>>
>>
>

[ccp4bb] AW: Could this be a complex crystal? or only RNA crystal? or micromolecular？

[Herman . Schreuder]

Dear Rachel,

You don’t have any spots with a resolution lower than ca. 15Å, which means that 
none of the cell axes can be longer than 15Å. This must be a crystal of some 
small molecule and not of a protein and/or RNA molecule.

One question: you mention that the data could not be processed by HKL2000; 
where did then the unit cell you quote come from? You could try indexing your 
data with small-molecule settings, e.g. allowing a very small unit cell.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Liu 
Rachel
Gesendet: Donnerstag, 15. Dezember 2016 18:54
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Could this be a complex crystal? or only RNA crystal? or 
micromolecular？




Dear everyone:



Recently, I suffered a problem during my research work. I co-purified a 
zinc finger protein(152aa) and a dsRNA(19bp), the final SEC buffer is 20mM 
Hepes, 150mM NaCl, pH8.0. Then the complex was co-crystallized by vapor 
diffusion against a solution of 30% PEG400, 0.2M MgCl, 0.1M Tris pH8.4.  The 
crystal is very beautiful, but the X-ray diffraction diagram is very strange, 
the diffraction point looks big and sparse(as shown in the picture). The Data 
cannot be processed with HKL2000 either.

 unit_cell = 24.808 42.863 119.042 90 90 90

 space_group = "I 2 2 2"



I wanna figure out, could this be a complex crystal? or only RNA crystal? 
or other micromolecular?



PS. I've set drops without the protein in the sample, but prepare the 
sample of RNA with the protein buffer as if the protein was there. And there 
was no crystallization .



Thank you very much!






Rachel Liu

Room 2071, research center in life sciences,

China Agricultural University

No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193  P.R. China

Tel: (86)-10-62734078