date:20180305

[ccp4bb] PhD position in the Leicester Institute of Structural and Chemical Biology

2018-03-05 Thread De Biasio, Alfredo (Dr.)



Dear colleagues,

My lab is hiring a highly motivated PhD student interested in biochemistry and 
structural biology of DNA replication proteins. The lab is located in the 
Leicester Institute of Structural and Chemical Biology (LISCB), which hosts a 
new Cryo-EM facility featuring a 300keV Titan Krios microscope with direct 
electron-detecting cameras. For further information please visit: 
https://www.findaphd.com/search/ProjectDetails.aspx?PJID=95592.  Please send 
your CV to ad...@leicester.ac.uk.


Best regards,

Dr. Alfredo De Biasio
Lecturer
Leicester Institute of Structural and Chemical Biology (LISCB)
Department of Molecular and Cell Biology
Henry Wellcome Building
University of Leicester,
Lancaster Road,
Leicester, LE1 7RH, UK
t: +44 (0)116 252 5391
e: ad...@leicester.ac.uk
   alfredo.debia...@gmail.com

[ccp4bb] CCP-EM Spring Symposium IV: 11-12th April 2018 - Registration now closes Wed 7th March

2018-03-05 Thread Tom Burnley

Dear all,

Due to the recent bad weather we have extended the registration period for
the Spring Symposium: it will now close this Wednesday (7th March).  Please
do register by then if you would to attend:

http://www.cvent.com/d/9tq4ln

This conference aims to provide a forum to highlight state of the art
developments in computational cryoEM and related themes as well as
showcasing outstanding recent applications. We promote an inclusive,
friendly atmosphere welcoming both old and new to the community. Topics
range from detector developments, image processing, single particle
reconstruction, high resolution model building & validation, machine
learning, tomography and electron diffraction.

The conference will be held 11-12th April at Keele University 2018
conference centre. Confirmed speakers include:

Mark Basham (Diamond)
SuRVoS: software for volume segmentation.
https://diamondlightsource.github.io/SuRVoS/

Sacha de Carlo (Dectris)
Detector technologies for high-resolution TEMs.

Ana Casanal (MRC-LMB)
Architecture of eukaryotic mRNA 3′-end processing machinery.
http://science.sciencemag.org/content/358/6366/1056.full

Peter Cherepanov (Crick Institute)
A supramolecular assembly mediates lentiviral DNA integration.
http://science.sciencemag.org/content/355/6320/93.long

Paul Emsley (MRC-LMB)
Coot model-building.
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Hans-Werner Fink (Zurich University)
“Holography with Low-Energy Electrons: a Tool for Single Molecule
Structural Biology.”
http://www.pnas.org/content/114/7/1474

Achilleas Frangakis (Goethe University Frankfurt)
“Image reconstruction and reliability algorithms for electron tomography.”

Tim Gruene (Paul Scherrer Institut)
"Collecting Diffraction Data with an Electron Microscope."

Nicola Guerrini (STFC)
Direct electron detector development at STFC from the Falcon and beyond.

Ben Himes (Janelia)
emClarity: software for sub-tomogram alignment and classification for
hetrogeneous specimens.
https://www.biorxiv.org/content/early/2017/12/08/231605

Arjen Jakobi (TU Delft)
“Improving density interpretation by local sharpening of cryo-EM density
maps.”
https://git.embl.de/jakobi/LocScale https://elifesciences
.org/articles/27131

Corinne Smith (University of Warwick)
"Defining clathrin cage interactions using high resolution cryoEM."

Carlos Oscar Sanchez Sorzano (CSIC Madrid)
"Complex Image Processing Workflows and High resolution reconstructions
using Scipion."
http://scipion.i2pc.es/

Chris Russo (MRC-LMB)
Ewald sphere correction using a single side-band image processing
algorithm.
https://www.sciencedirect.com/science/article/pii/S030439911730431X
Charge accumulation in electron cryomicroscopy.
https://www.sciencedirect.com/science/article/pii/S0304399117304291
Microscopic charge fluctuations cause minimal contrast loss in cryoEM.
https://www.sciencedirect.com/science/article/pii/S0304399117304308

Beata Turonova (EMBL)
Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF
improves subtomogram averaging resolution to 3.4 Å.
https://doi.org/10.1016/j.jsb.2017.07.007

Giulia Zanetti (Birkbeck)
"Coat protein complexes studied by cryo-tomography and sub-tomogram
averaging."

Kai Zhang (MRC-LMB)
Gctf: real-time CTF determination and correction.
https://dx.doi.org/10.1016%2Fj.jsb.2015.11.003

Xiaodong Zhang (Imperial)
"High resolution complexes determined by SPR EM." [Final title to be
confirmed.]

Plus what's new at CCP-EM, EBI and eBIC

Registrations close Friday 2nd March.

Registration site:
http://www.cvent.com/d/9tq4ln

Registration fees:
PI/Industrial: £175.00
Student/PostDoc: £100.00

We have also ensured reasonably priced accommodation is available from Keele
University (£70/room/night; available on registration).

Best wishes,

Tom, Helen, Colin & Martyn


-- 
Dr Tom Burnley, PhD
CCP-EM | @ccp_em * | *www.ccpem.ac.uk

Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] Small molecule not refined in coot.

2018-03-05 Thread M T

Dear all,

I am actually dealing with a structure containing an unnatural ligand.
I generated the pdb file by drawing it on PRODRG server, I did a manual
pre-fit in the map using coot and I manually merged the pdf file of my
protein with the one of the ligand.
After that I did few cycles of refinement using Refmac5, with my mtz, my
merged pdb file and the cif library of the ligand as input files.

First I saw that even if Refmac "completed succesfully" it didn't modify
coordinates of the ligand, second I saw a warning about the "DRG" molecule
in the log of Refmac (WARNING: duplicated name of monomer DRG Last entry
will be used.), third in Coot I cannot use "Real Space Refine Zone" with
the ligand and when I try to import the CIF dictionary produced by PRODRG
(through the server or even the one generated through CCP4 ProDrg), it
causes Coot crash (** (coot-bin:4467): WARNING **: Widget not found:
cif_dictionary_file_selector_create_molecule_checkbutton
/programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288:  4467 Segmentation
fault: 11  $coot_bin "$@").

Clearly I am not a skilled user of all these programs, so I certainly did
a/some mistake/s, but if someone can give me tips to be able to refine my
ligand... Should I rename my DRG molecule, should I verify particular
things, should I use other ways to generate the pdb and the library of my
ligand?

Thank you.

P.S.: I am running CCP4 and coot using SBGRID on a Mac.

Michel

Re: [ccp4bb] Small molecule not refined in coot.

2018-03-05 Thread Colin Levy

Hi Michel,

If your ligand is designated as DRG in your pdb then refinement programs will 
anticipate that it is:

Chemical Description
Name5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
Formula C12 H11 N3
Formal charge   0
Molecular weight197.236 g/mol
Component type  NON-POLYMER


If this is not the case then you need to choose a unique identifier, this 
should then allow your cif library to be utilised appropriately during 
refinement.

Colin


[cid:3A59087A-E871-4A15-8C7F-384F6788170E@man.ac.uk]



Dr. Colin W. Levy
MIB G016
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk

 Manchester Institute of Biotechnology | University of Manchester | 3.020 
Garside Building | 131 Princess Street | Manchester | M1 7DN

[cid:image001.png@01D11BB1.F717D2B0][cid:image002.png@01D11BB1.F717D2B0][cid:image003.png@01D11BB1.F717D2B0][cid:image004.png@01D11BB1.F717D2B0][cid:image005.png@01D11BB1.F717D2B0]








On 5 Mar 2018, at 12:30, M T mailto:michel...@gmail.com>> 
wrote:

Dear all,

I am actually dealing with a structure containing an unnatural ligand.
I generated the pdb file by drawing it on PRODRG server, I did a manual pre-fit 
in the map using coot and I manually merged the pdf file of my protein with the 
one of the ligand.
After that I did few cycles of refinement using Refmac5, with my mtz, my merged 
pdb file and the cif library of the ligand as input files.

First I saw that even if Refmac "completed succesfully" it didn't modify 
coordinates of the ligand, second I saw a warning about the "DRG" molecule in 
the log of Refmac (WARNING: duplicated name of monomer DRG Last entry will be 
used.), third in Coot I cannot use "Real Space Refine Zone" with the ligand and 
when I try to import the CIF dictionary produced by PRODRG (through the server 
or even the one generated through CCP4 ProDrg), it causes Coot crash (** 
(coot-bin:4467): WARNING **: Widget not found: 
cif_dictionary_file_selector_create_molecule_checkbutton 
/programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288:  4467 Segmentation 
fault: 11  $coot_bin "$@").

Clearly I am not a skilled user of all these programs, so I certainly did 
a/some mistake/s, but if someone can give me tips to be able to refine my 
ligand... Should I rename my DRG molecule, should I verify particular things, 
should I use other ways to generate the pdb and the library of my ligand?

Thank you.

P.S.: I am running CCP4 and coot using SBGRID on a Mac.

Michel

[ccp4bb] Interfaces

2018-03-05 Thread Lorenzo Briganti

Good morning all,


I need to identify my dimer and tetramer interfaces, and point them out in 
Pymol. Any website/program/script suggestions? I tried PISA, but it only shows 
me some residues from some interfaces, I need something more "complete".


Thank you very much,


Lorenzo

Re: [ccp4bb] Interfaces

2018-03-05 Thread Eugene Valkov

Can you define "more complete"? What information do you require that PISA
does not provide?

This way you may get specific recommendations/suggestions.

Eugene


On 5 March 2018 at 14:02, Lorenzo Briganti 
wrote:

> Good morning all,
>
>
> I need to identify my dimer and tetramer interfaces, and point them out in
> Pymol. Any website/program/script suggestions? I tried PISA, but it only
> shows me some residues from some interfaces, I need something more
> "complete".
>
>
> Thank you very much,
>
>
> Lorenzo
>

[ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-05 Thread Herman . Schreuder

Hi Colin and Michel,

In my experience, both refmac and coot will use the most recently read-in cif
dictionary and there is no need to try to find an unique identifier for each
new ligand one uses. The new dictionary overrides the old one. Finding a unique
identifier for each new ligand would be a terrible and unnecessary hassle.

What usually goes wrong is that the name of the residue in the pdb file does
not match the name of the residue in the cif file. And the same holds for the
atom names. I would check with an editor that the resdue and atom names of the
pdb file do match the residue and atom names in the cif dictionary.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Colin
Levy
Gesendet: Montag, 5. März 2018 13:38
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Small molecule not refined in coot.

Hi Michel,

If your ligand is designated as DRG in your pdb then refinement programs will
anticipate that it is:

Chemical Description
Name

5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE

Formula

C12 H11 N3

Formal charge

Molecular weight

197.236 g/mol

Component type

NON-POLYMER

If this is not the case then you need to choose a unique identifier, this
should then allow your cif library to be utilised appropriately during
refinement.

Colin

[cid:image006.png@01D3B48E.20BC8DA0]

Dr. Colin W. Levy
MIB G016
Tel. 0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk

[cid:image007.png@01D3B48E.20BC8DA0][cid:image008.png@01D3B48E.20BC8DA0][cid:image009.png@01D3B48E.20BC8DA0][cid:image010.png@01D3B48E.20BC8DA0][cid:image011.png@01D3B48E.20BC8DA0]

On 5 Mar 2018, at 12:30, M T mailto:michel...@gmail.com>>
wrote:

Dear all,
I am actually dealing with a structure containing an unnatural ligand.
I generated the pdb file by drawing it on PRODRG server, I did a manual pre-fit
in the map using coot and I manually merged the pdf file of my protein with the
one of the ligand.
After that I did few cycles of refinement using Refmac5, with my mtz, my merged
pdb file and the cif library of the ligand as input files.
First I saw that even if Refmac "completed succesfully" it didn't modify
coordinates of the ligand, second I saw a warning about the "DRG" molecule in
the log of Refmac (WARNING: duplicated name of monomer DRG Last entry will be
used.), third in Coot I cannot use "Real Space Refine Zone" with the ligand and
when I try to import the CIF dictionary produced by PRODRG (through the server
or even the one generated through CCP4 ProDrg), it causes Coot crash (**
(coot-bin:4467): WARNING **: Wi

[ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-05 Thread Herman . Schreuder

PS: If you have two different home-brewn ligands, you have to rename one of
them (pdb and cif), otherwise the same dictionary will be applied to two
different ligands. Also make sure your cif file is a dictionary and not just a
coordinate file.
HS

Von: Schreuder, Herman /DE
Gesendet: Montag, 5. März 2018 14:31
An: 'Colin Levy'; CCP4BB@JISCMAIL.AC.UK
Betreff: AW: [ccp4bb] Small molecule not refined in coot.

Hi Colin and Michel,

Best,
Herman

Hi Michel,

If your ligand is designated as DRG in your pdb then refinement programs will
anticipate that it is:

Chemical Description
Name

5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE

Formula

C12 H11 N3

Formal charge

Molecular weight

197.236 g/mol

Component type

NON-POLYMER

If this is not the case then you need to choose a unique identifier, this
should then allow your cif library to be utilised appropriately during
refinement.

Colin

[cid:image001.png@01D3B48F.5E6EF790]

Dr. Colin W. Levy
MIB G016
Tel. 0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk

[cid:image002.png@01D3B48F.5E6EF790][cid:image003.png@01D3B48F.5E6EF790][cid:image004.png@01D3B48F.5E6EF790][cid:image005.png@01D3B48F.5E6EF790][cid:image006.png@01D3B48F.5E6EF790]

On 5 Mar 2018, at 12:30, M T mailto:michel...@gmail.com>>
wrote:

[ccp4bb] help

2018-03-05 Thread Chandra


Hello all

Does anyone knows of a review that highlights the first examples of the 
use of NMR combined with X-ray crystallography to solve the structures 
of proteins


thanks

chandra

[ccp4bb] Residential School on Medicinal Chemistry and Biology in Drug Discovery (ResMed): A Comprehensive One-Week Course

2018-03-05 Thread Strickland, Corey

All,

I was asked by the meeting organizers to let the CCP4 community 
know about the 2018 Residential School on Medicinal Chemistry and Biology in 
Drug Discovery.See below for information about the course and contact 
information.

Sincerely,
Corey

-
Dear all,

The 32nd Annual ResMed: Residential School on Medicinal Chemistry and Biology 
in Drug Discovery, www.drew.edu/resmed will be held 
on June 10 - June 15, 2018 at Drew University, Madison NJ.  However, all 
resident attendees will be staying at The Madison 
Hotel, with further accommodations provided at 
the Morristown 
Inn 
as needed. There will be a shuttle to transport attendees to and from the 
campus. ResMed is co-sponsored by the ACS MEDI Division.

ResMed is a week-long graduate level course organized to provide an accelerated 
program for chemists, biologists and other industrial and academic scientists 
who wish to broaden their knowledge of drug discovery and development.  The 
School's aim is to concentrate on the fundamentals that are useful in drug 
discovery spanning initial target validation through clinical development. The 
program provides ample opportunity for discussions with distinguished faculty 
from industry and academia.

The purpose of the School is to provide a strong background in the principles 
of drug discovery and development to enhance collaborative drug discovery 
programs. Previous attendees with backgrounds in macromolecular crystallography 
have found the course of great value in their research projects.

The tuition rate for Hotel Residents will include hotel stay, ResMed tuition, 
course materials, and all meals. Information regarding ResMed can be accessed 
on our website: www.drew.edu/resmed including our 
program and application.

Please join us in our 32nd year. We look forward to seeing you.

Sincerely,
Co-organizers,
William J. Greenlee, Ph.D
Vincent P. Gullo, Ph.D.
Ronald J. Doll, Ph.D.
Marvin Bayne, Ph.D.

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey, USA 07033), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

2018-03-05 Thread Eleanor Dodson

Herman is right - as long as refmac reads your generated DRG that is the
dictionary it will use..

My way of doing this sort of thing:

Start with COOT with the DRG coordinates and ProDRG dictionary and try a
bit of real space refinement.
Coot should move the coodinates a bit and you should see something happen.

Then read out those new coordinates and run refmac. Again the coords should
move a bit, and at lest the B factors should change. If REFMAC dooesnt like
your naming it will report it..

Again if COOT accepted the dictionary the first time I cant see why it wont
read it again. are you sure you are finding the same cif file?

You will have to read your own DRG into coot or otherwise it will find
something which is not appropriate for your problem..
Eleeanor

On 5 March 2018 at 13:36,  wrote:

> PS: If you have two different home-brewn ligands, you have to rename one
> of them (pdb and cif), otherwise the same dictionary will be applied to two
> different ligands. Also make sure your cif file is a dictionary and not
> just a coordinate file.
>
> HS
>
>
>
> *Von:* Schreuder, Herman /DE
> *Gesendet:* Montag, 5. März 2018 14:31
> *An:* 'Colin Levy'; CCP4BB@JISCMAIL.AC.UK
> *Betreff:* AW: [ccp4bb] Small molecule not refined in coot.
>
>
>
> Hi Colin and Michel,
>
>
>
> In my experience, both refmac and coot will use the most recently read-in
> cif dictionary and there is no need to try to find an unique identifier for
> each new ligand one uses. The new dictionary overrides the old one. Finding
> a unique identifier for each new ligand would be a terrible and unnecessary
> hassle.
>
>
>
> What usually goes wrong is that the name of the residue in the pdb file
> does not match the name of the residue in the cif file. And the same holds
> for the atom names. I would check with an editor that the resdue and atom
> names of the pdb file do match the residue and atom names in the cif
> dictionary.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] *Im Auftrag von *Colin Levy
> *Gesendet:* Montag, 5. März 2018 13:38
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Small molecule not refined in coot.
>
>
>
> Hi Michel,
>
>
>
> If your ligand is designated as DRG in your pdb then refinement programs
> will anticipate that it is:
>
>
> Chemical Description
>
> *Name*
>
> 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
>
> *Formula*
>
> C12 H11 N3
>
> *Formal charge*
>
> 0
>
> *Molecular weight*
>
> 197.236 g/mol
>
> *Component type*
>
> NON-POLYMER
>
>
>
>
>
> If this is not the case then you need to choose a unique identifier, this
> should then allow your cif library to be utilised appropriately during
> refinement.
>
>
>
> Colin
>
>
>
>
>
>
>
> Dr. Colin W. Levy
>
> MIB G016
>
> Tel.  0161 275 5090
>
> Mob.07786 197 554
> c.l...@manchester.ac.uk
>
>
>
>  Manchester Institute of Biotechnology | University of Manchester | 3.020
> Garside Building | 131 Princess Street | Manchester | M1 7DN
> 
>
>
>
> 
> 
> 
> 
> 
>
>
>
>
>
>
>
>

Re: [ccp4bb] help

2018-03-05 Thread Eleanor Dodson

Llok at this paper:

Does NMR Mean “Not for Molecular Replacement”? Using NMR-Based Search
Models to Solve Protein Crystal Structures

The references there clainm to give the first instance of success...

And Hi Eleanor

On 5 March 2018 at 13:51, Chandra  wrote:

> Hello all
>
> Does anyone knows of a review that highlights the first examples of the
> use of NMR combined with X-ray crystallography to solve the structures of
> proteins
>
> thanks
>
> chandra
>

[ccp4bb] Postdoctoral Position in Structural Biology

2018-03-05 Thread Yousif Shamoo

Postdoctoral Position in Biochemistry and X-ray Crystallography

At Rice University

A postdoctoral position in structural biology is available in the Shamoo Lab
at Rice University.  The successful candidate must have experience in X-ray
crystallography as well as biochemistry. Candidates should hold a PhD degree
in biophysics or biochemistry and have a good publication record.

Additional useful experience in one or more of these technical areas is also
desirable:

* Protein purification

* Enzyme kinetics

* Ligand (DNA/RNA) binding studies

Our group studies the evolution of antibiotic resistance in clinical
pathogens. We use a combination of experimental evolution, genomics and
biochemical approaches to understand the biophysical basis for newly evolved
resistances. Experience with writing manuscripts and grants is also
desirable. Candidates must also have very good interpersonal skills to work
in our highly interdisciplinary research team and be able to assist in the
mentoring of students. 

Interested candidates should send a cover letter, CV and the names of three
references to sha...@rice.edu

 

 

Yousif Shamoo, Ph.D.

Rice University

Vice Provost for Research

Professor, Department of Biosciences

MS-603

P.O. Box 1892

Houston, TX. 77251-1892

(Ph) 713-348-5493

(F) 713-348-4105

Re: [ccp4bb] A helix with leucine repeats

2018-03-05 Thread Emilia C. Arturo (Emily)

Could it be a member of a coiled coil at some point in its lifetime, as a
part of its function in regulating position or activity of this receptor?
Does the helix have sequence similarity to other coiled coils? see
https://www.uniprot.org/help/coiled for a primer on the topic.

Looks fun!

Emily.



On Sun, Mar 4, 2018 at 5:01 PM, Cheng Zhang  wrote:

> Hi Michael,
>
> Thanks for the information.
>
> It is amphipathic. It follows a transmembrane helical domain of a cell
> surface receptor and adopts an orientation parallel to the membrane. So it
> may be associated with the membrane. I am just wondering if such
> leucine-repeat motif is special among all amphipathic, membrane-associated
> helical structures. In other words, any other possible functional roles
> than just membrane association?
>
> Best,
>
> Cheng
>
>
> On Sat, Mar 3, 2018 at 10:23 PM, R. Michael Garavito  > wrote:
>
>> Dear Cheng,
>>
>> Chris and Ruud have provided you with the typical interpretation of such
>> a motif, but you have forgotten to give the CCP4 community the context of
>> this leucine-repeat helix.  Is it amphipathic?  Does the protein also have
>> transmembrane helices (as suggested by the figure provided) which would
>> provide the membrane anchoring?
>>
>> Look up structurally similar membrane proteins (not necessarily
>> homologous by sequence), such as proteins which have a monotonic-like
>> membrane interaction, but that also have a transmembrane helix (monoamine
>> oxidase or some mammalian cyt P450s).  If your protein is monotopic, look
>> at that class of membrane proteins (squalene cyclase, fatty acid hydrolase,
>> cyclooxygenase, etc.).  One structurally undescribed motif is a “reentrant
>> membrane helix.”  In other words, look at context before assigning
>> function.
>>
>> Good luck and hope this helps,
>>
>> Michael
>>
>> **
>>
>> *R. Michael Garavito, Ph.D.*
>>
>> *Professor of Biochemistry & Molecular Biology*
>>
>> *513 Biochemistry Bldg.   *
>>
>> *Michigan State University  *
>>
>> *East Lansing, MI 48824-1319*
>>
>> *Office:*  *(517) 355-9724 <(517)%20355-9724> Lab:  (517) 353-9125
>> <(517)%20353-9125>*
>>
>> *FAX:  (517) 353-9334 <(517)%20353-9334>Email:
>> rmgarav...@gmail.com *
>>
>> **
>>
>>
>>
>> On Mar 3, 2018, at 3:51 PM, Cheng Zhang > > wrote:
>>
>> Hi all,
>>
>> We recently got a structure of a transmembrane protein. There is a helix
>> that is parallel to the membrane. The function of this helix is not known
>> and we are trying to make some hypothesis. A unique feature is that there
>> are repeated leucine residues on this helix facing the lipids. I am
>> wondering if anyone has seen a similar pattern and could suggest possible
>> function, e.g. membrane anchoring?
>>
>> Thanks!
>>
>> Best,
>>
>> Cheng
>>
>> 
>>
>>
>> --
>> -
>> Cheng Zhang
>>
>>
>>
>
>
> --
> -
> Cheng Zhang
>



-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May
Alcott

[ccp4bb] Postdoctoral Position

2018-03-05 Thread Elżbieta Nowak

POSTDOCTORAL FELLOW POSITION AVAILABLE

at the Laboratory of Protein Structure of
INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY in Warsaw, Poland.

Laboratory of Protein Structure seeks a researcher with a PhD degree to study
the mechanisms of DNA repair.

Laboratory Interest
Laboratory of Protein Structure focuses on structural and biochemical studies
of nucleic acid enzymes using protein crystallography and cryo-electron
microscopy as a primary methods. More information can be found at
https://www.iimcb.gov.pl/en/research/laboratories/6-laboratory-ofprotein-structure-nowotny-laboratory#tab2

Profile of candidates/requirements:

1. PhD degree in biological sciences or related fields, obtained not earlier
than in 2011
2. Solid knowledge and documented laboratory experience in at least one of the
following disciplines: structural biology, molecular biology, biochemistry
3. Very good command of English (oral and written)

4. Motivation and passion for experimental work

Interested candidates are kindly asked to provide short motivation letter, CV
and the name of a referee by April 1st, 2018 . Application should be submitted
to pr...@iimcb.gov.pl titled: postdoc_MAESTRO_LSB. The shortlisted candidates
will be contacted regarding further selection procedures.

Elzbieta Nowak Ph.D.

***
Laboratory of Protein Structure
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street,
02-109 Warsaw, Poland
Telephone: (+48 22) 597 07 21
Fax: (+48 22) 597 07 15

[ccp4bb] PhD student position available

2018-03-05 Thread Elżbieta Nowak

PhD STUDENT POSITION AVAILABLE

at the Laboratory of Protein Structure of
INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY in Warsaw, Poland.

Laboratory of Protein Structure seeks PhD student to study the mechanisms of
DNA repair. PhD fellowship is funded in frame of National Science Centre
MAESTRO grant.

Laboratory Interest
Laboratory of Protein Structure focuses on structural and biochemical studies
of nucleic acid enzymes using protein crystallography and cryo-electron
microscopy as a primary methods. More
information can be found at :
https://www.iimcb.gov.pl/en/research/laboratories/6-laboratory-ofprotein-structure-nowotny-laboratory#tab2

Key responsibilities include
The production of protein using different expression systems, purification of
proteins, crystallization and structure determination by crystallography and/or
cryo-EM. Biochemical studies of DNA repair proteins.

Profile of candidates/requirements:
1. Solid knowledge and documented laboratory experience in at least one of the
following disciplines: structural biology, molecular biology, biochemistry
2. Very good command of English (oral and written)

3.. Motivation and passion for experimental work

Interested candidates are kindly asked to provide short motivation letter, CV
and the name of a referee by April 1st, 2018 . Application should be submitted
to pr...@iimcb.gov.pl titled: PhDstudent_MAESTRO_LSB. The shortlisted
candidates will be contacted regarding further selection procedures.

Elzbieta Nowak Ph.D.

***
Laboratory of Protein Structure
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street,
02-109 Warsaw, Poland
Telephone: (+48 22) 597 07 21
Fax: (+48 22) 597 07 15

Re: [ccp4bb] does 12 A diffraction worth optimization

2018-03-05 Thread Phoebe A. Rice

In addition to the other useful advice offered, I’d also suggest determining if 
the whole complex or just the DNA fits in the asymmetric unit.  Particularly if 
the crystals are hexagonal rods or plates, you might have DNA-only crystals.

~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
  Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/


From: CCP4 bulletin board  on behalf of Natalia O 

Reply-To: Natalia O 
Date: Friday, March 2, 2018 at 7:35 PM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] does 12 A diffraction worth optimization

Hello,

I got crystals of protein-nucleic acid complex, rod-shape, reproducible, don’t 
visibly get damaged upon freezing; however they gave diffraction only to about 
12 A. I tried several crystals. My question is whether such crystals worth 
optimization. Clearly a 4A diffracting crystal could potentially be optimized 
to 3 – 2.5A, but if the diffraction that I am getting now is 12A it could 
suggest that the system is so flexible that getting to 3A with this crystal 
form is not possible at all. I just wonder if there is any statistics or a rule 
of thumb about what initial diffraction worth optimization?

Thank you!
-Natalia

[ccp4bb] 2x Postdoctoral Positions in Structural Biology

2018-03-05 Thread Andrew Ellisdon

Hi All,

We are seeking two junior postdoctoral researchers with demonstrated
expertise in biochemistry and structural biology and an interest in the
structure and function of ligand:receptor and antibody:receptor complexes
in immunity. The appointment will be based at the Monash University
Biomedicine Discovery Institute in Melbourne, Australia.

The team have regular access to the Australian Synchrotron and cryo-EM
microscopes including a Titan Krios (K2) and a Talos Arctica (F3).
Experience or a willingness to learn single-particle cryo-EM would be
highly valuable. The successful applicants are expected to have strong
potential to develop into leaders of independent research programs.

Further details:

https://www.monash.edu/__data/assets/pdf_file/0005/1216184/Cancer-Andrew-Ellisdon-updated.pdf


http://careers.pageuppeople.com/513/cw/en/job/575147/research-fellow-biochemistry-and-molecular-biology



Applications close Thursday 15th March 2018.

Regards,
Andrew Ellisdon

Enquiries about these positions should be sent to:andrew.ellis...@monash.edu

[ccp4bb] Off-topic question

2018-03-05 Thread Jobichen Chacko

Dear All,
We are trying to identify/sequence a DNA/RNA fragment (around 100bp) which
was co-purified along with our protein.
The expression was done in E.coli.
Any suggestions on how to do this.
Thank you.
Jobi

Re: [ccp4bb] Off-topic question

2018-03-05 Thread Philippe BENAS

Hi Jobi,
Phenol/CHCl3 extraction, iPrOH precipitation and then nucleic acid sequencing.

Best regards,Philippe Philippe BENAS, Ph.D.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Jobichen Chacko 
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Mardi 6 mars 2018 5h11
 Objet : [ccp4bb] Off-topic question
   
Dear All,
We are trying to identify/sequence a DNA/RNA fragment (around 100bp) which was 
co-purified along with our protein.
The expression was done in E.coli.
Any suggestions on how to do this.
Thank you.
Jobi

Re: [ccp4bb] Off-topic question

2018-03-05 Thread Debanu Das

Hi,
I was going to suggest the same but since it has already been said, here’s a 
cheeky suggestion: you could try determining the crystal structure of the 
complex and get a direct sequence readout for the nuclei acid.
Best,
Debanu 

> On Mar 5, 2018, at 9:34 PM, Philippe BENAS 
> <0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Jobi,
> 
> Phenol/CHCl3 extraction, iPrOH precipitation and then nucleic acid sequencing.
> 
> Best regards,
> Philippe
>  
> Philippe BENAS, Ph.D.
> 
> Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
> Faculté de Pharmacie, Université Paris Descartes
> Case 48
> Av, de l'Observatoire
> F-75270 PARIS cedex 06
> +33.1.5373.1599
> E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
> URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
> http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
> 
> 
> 
> De : Jobichen Chacko 
> À : CCP4BB@JISCMAIL.AC.UK 
> Envoyé le : Mardi 6 mars 2018 5h11
> Objet : [ccp4bb] Off-topic question
> 
> Dear All,
> We are trying to identify/sequence a DNA/RNA fragment (around 100bp) which 
> was co-purified along with our protein.
> The expression was done in E.coli.
> Any suggestions on how to do this.
> Thank you.
> Jobi
> 
>

[ccp4bb] PhD position in the Leicester Institute of Structural and Chemical Biology

[ccp4bb] CCP-EM Spring Symposium IV: 11-12th April 2018 - Registration now closes Wed 7th March

[ccp4bb] Small molecule not refined in coot.

Re: [ccp4bb] Small molecule not refined in coot.

[ccp4bb] Interfaces

Re: [ccp4bb] Interfaces

[ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

[ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

[ccp4bb] help

[ccp4bb] Residential School on Medicinal Chemistry and Biology in Drug Discovery (ResMed): A Comprehensive One-Week Course

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

Re: [ccp4bb] help

[ccp4bb] Postdoctoral Position in Structural Biology

Re: [ccp4bb] A helix with leucine repeats

[ccp4bb] Postdoctoral Position

[ccp4bb] PhD student position available

Re: [ccp4bb] does 12 A diffraction worth optimization

[ccp4bb] 2x Postdoctoral Positions in Structural Biology

[ccp4bb] Off-topic question

Re: [ccp4bb] Off-topic question

Re: [ccp4bb] Off-topic question

21 matches

Site Navigation

Mail list logo

Footer information