Hi Aaron, thank you for your tribute to an extraordinary scientist; It brought
back happy memories.
Jack Dunitz visited Australia in the late ‘80s, possibly for the IUCr meeting
in Perth, and I can recall his razor wit and much hilarity when he, Sandy
Mathieson, and Jim Morrison were recalling their early days in science.
Vale Jack.
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of CCP4BB automatic
digest system <lists...@jiscmail.ac.uk>
Date: Thursday, 16 September 2021 at 02:15
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: CCP4BB Digest - 14 Sep 2021 to 15 Sep 2021 - Special issue (#2021-265)
There are 9 messages totaling 130442 lines in this issue.
Topics in this special issue:
1. Prof. Jack Dunitz, 1923-2021
2. software DS, fconv still available ? contact?
3. Call for EMBL Hamburg Synchrotron Beamtime Applications
4. Phosphatase enzymatic assay (3)
5. AW: Phosphatase enzymatic assay
6. MX-RDR - Macromolecular Xtallography Raw Data Repository
7. Postdoctoral Research Opportunity in Cryo-EM at University of Washington,
in Seattle, USA
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Date: Tue, 14 Sep 2021 22:18:48 -0700
From: Robert Stroud <str...@msg.ucsf.edu>
Subject: Re: Prof. Jack Dunitz, 1923-2021
Thanks Aaron, a beautiful recognition of a great scientist.
Robert Stroud
str...@msg.ucsf.edu
> On Sep 14, 2021, at 10:13 AM, Aaron Finke <af...@cornell.edu> wrote:
>
> Dear all,
>
> It is with a heavy heart that I announce the passing of Prof. Jack Dunitz at
> the age of 98. Prof. Dunitz was a giant in the development of modern
> crystallographic methods, most notably in the determination of the crystal
> structure of ferrocene, confirming the “sandwich complex” nature of that
> molecule and ushering in the field of organometallic chemistry. As a
> crystallographer, mathematician, and chemist, Prof. Dunitz effectively
> bridged the gap between crystallography and chemistry, inspiring chemists to
> exploit the utility of the burgeoning field of crystallography. He was a
> professor at ETH-Zurich for over 60 years, and even after his “retirement” in
> 1990, dedicated his life to crystallographic research.
>
> I have many fond memories of Prof. Dunitz from my time at ETH. Even at the
> age of 91, he still came into the office at least three times a week to
> pursue research programs; I am told he continued to come in regularly until
> Covid forced the campus closed. His wit and curiosity never dulled, and was
> enamored with new technologies that enabled various new forms of
> crystallographic research. He owned an iPad before I ever did! As a postdoc
> doing crystallography, Prof. Dunitz enjoyed calling me into his office,
> ostensibly to help him use some feature of CCDC Mercury, but in reality to
> discuss some new idea he had about crystal symmetry and exploiting it to gain
> some greater understanding of coordination complexes. He was the kind of
> person who had forgotten more chemistry than I will ever know, and these
> discussions were always enlightening and entertaining, mixing new theory with
> the history of crystallography, much of which he bore witness or contributed
> to. He will be sorely missed.
>
> If you would like to express your condolences, please use the following email
> address: jack_condole...@ethz.ch <mailto:jack_condole...@ethz.ch>
>
> Aaron
> ------------------------------------------
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu <mailto:af...@cornell.edu>
>
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------------------------------
Date: Wed, 15 Sep 2021 09:25:48 +0200
From: Guenter Fritz <guenter.fritz.phenix.c...@gmail.com>
Subject: Re: software DS, fconv still available ? contact?
Dear Manfred,
thanks a lot. I had checked the homepage before. There is a note that
the software is not any more available for download from their site.
But no further hint whether it is available somewhere else.
Best regards,
Guenter
> https://agklebe.pharmazie.uni-marburg.de/
>
> Cheers,
> Manfred
>
> Am 14.09.2021 um 14:36 schrieb Guenter Fritz:
>> Dear all,
>>
>> does somebody know whom to contact for the software DSX or fconv of
>> the former group Klebe in Marburg?
>>
>> Many thanks and best regards,
>>
>> Guenter
>>
>> ########################################################################
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>
> --
> Dr. Manfred S. Weiss
> Macromolecular Crystallography
> Helmholtz-Zentrum Berlin
> Albert-Einstein-Str. 15
> D-12489 Berlin
> Germany
>
>
> ________________________________
>
> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
>
> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
> Forschungszentren e.V.
>
> Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr.
> Jutta Koch-Unterseher
> Geschäftsführung: Prof. Dr. Jan Lüning (Sprecher), Prof. Dr. Bernd
> Rech, Thomas Frederking
>
> Sitz Berlin, AG Charlottenburg, 89 HRB 5583
>
> Postadresse:
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> 14109 Berlin
> Deutschland
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------------------------------
Date: Wed, 15 Sep 2021 12:37:20 +0200
From: Ivanka Araujo <ivanka.ara...@embl-hamburg.de>
Subject: Call for EMBL Hamburg Synchrotron Beamtime Applications
We are glad to announce the call for synchrotron beamtime applications
in biological small-angle X-ray scattering (SAXS) and macromolecular
crystallography (MX) for the period February - December 2022. The
following EMBL beamlines at PETRA III are available: P12 (SAXS), P13 and
P14 including the T-REXX endstation (MX). For both SAXS and MX,
instrumentation for pump-probe time-resolved experiments is in place.
Submission of BAG (Block Allocation Group) proposals is strongly
encouraged for SAXS and MX. Groups applying for beamtime to work on
several projects during 2022 are requested to submit their research
proposals via a BAG application and not as several individual proposals
(even if the BAG only consists of a single research group).
Please bear in mind that remote and mail-in operation will remain the
default access route for all EMBL beamlines as long as necessary during
2022 due to the Corona pandemic.
Please note: COVID-19 related proposals requiring rapid access can be
submitted at any time; contact the User Office directly for more
information about the submission process.
The deadline for submission of proposals for 2022 is:
_*Monday, 18th October 2021 (midnight CET)*_.
After this date, the proposals will be evaluated by an external Project
Evaluation Committee and the users will be informed about the results of
their application(s) in early January 2022.
A detailed description of the three beamlines and links to the
electronic proposal forms can be found at:
SAXS: https://www.embl-hamburg.de/services/saxs/
<https://www.embl-hamburg.de/services/saxs/>
(see also
https://www.embl-hamburg.de/services/saxs/How_to_apply_for_BioSAXS_access.pdf
<https://www.embl-hamburg.de/services/saxs/How_to_apply_for_BioSAXS_access.pdf>)
MX: https://www.embl-hamburg.de/services/mx/
<https://www.embl-hamburg.de/services/mx/>
Time-resolved MX: https://www.embl-hamburg.de/services/mx/P14_EH2
<https://www.embl-hamburg.de/services/mx/P14_EH2>
Submit a proposal via the EMBL Hamburg user portal:
https://smis.embl-hamburg.de <https://smis.embl-hamburg.de>
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.
For further general information, please contact the EMBL Hamburg user
office:
Tel.: +49 40-89902-111/183/311
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 characterisation)
With kind regards,
EMBL Hamburg User Office
--
Ivanka Fernandes Araujo
European Molecular Biology Laboratory
c/o DESY
Notkestraße 85, Bldg. 48e
22607 Hamburg
Germany
Tel.: +49-40-89902-183
Fax: +49-40-89902-260
http://www.embl-hamburg.de
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------------------------------
Date: Wed, 15 Sep 2021 14:28:45 +0200
From: Andrea Moretti <andrea.more...@unige.ch>
Subject: Phosphatase enzymatic assay
Dear CCP4 community,
sorry for the off topic question but I am struggling with enzymatic
assays and I would need your help.
I am trying to measure dephosphorylation of a phosphorylated kinase by a
ser/thr phosphatase. So far I tried to measure it by malachite green
assay, anti pSer/pThr antibody and PNPase coupled assay but nothing
really worked for me. NMR is unfortunately not an option since I can't
make enough of the proteins.
So any hints on phosphatase assays would be helpful.
Thanks!
Best wishes,
Andrea
--
Andrea Moretti
Structural Plant Biology Laboratory
Department of Botany and Plant Biology
Sciences III
University of Geneva
30 Quai E. Ansermet
1211 Geneva
Switzerland
Email: andrea.more...@unige.ch
Phone: +41 22 379 3029 (office)
web:http://structplantbio.org
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------------------------------
Date: Wed, 15 Sep 2021 14:47:05 +0200
From: Wim Burmeister <wim.burmeis...@ibs.fr>
Subject: Re: Phosphatase enzymatic assay
Hello,
try mass spectrometry, either after tryptic digestion into peptides or
electrospray MS on the entire protein if it is not too big.
Best
Wim
----- Mail original -----
De: "Andrea Moretti" <andrea.more...@unige.ch>
À: "CCP4BB" <CCP4BB@JISCMAIL.AC.UK>
Envoyé: Mercredi 15 Septembre 2021 14:28:45
Objet: [ccp4bb] Phosphatase enzymatic assay
Dear CCP4 community,
sorry for the off topic question but I am struggling with enzymatic
assays and I would need your help.
I am trying to measure dephosphorylation of a phosphorylated kinase by a
ser/thr phosphatase. So far I tried to measure it by malachite green
assay, anti pSer/pThr antibody and PNPase coupled assay but nothing
really worked for me. NMR is unfortunately not an option since I can't
make enough of the proteins.
So any hints on phosphatase assays would be helpful.
Thanks!
Best wishes,
Andrea
--
Andrea Moretti
Structural Plant Biology Laboratory
Department of Botany and Plant Biology
Sciences III
University of Geneva
30 Quai E. Ansermet
1211 Geneva
Switzerland
Email: andrea.more...@unige.ch
Phone: +41 22 379 3029 (office)
web:http://structplantbio.org
########################################################################
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--
Wim Burmeister
Professor
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs / CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ]
Mobile: +33 (0) 7 50 49 19 91
[
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
| website ]
Changement climatique : «Les autres combats n’ont aucun sens si celui-là est
perdu» ( Aurélien Barrau )
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------------------------------
Date: Wed, 15 Sep 2021 09:11:51 -0400
From: Patrick Loll <pjl...@gmail.com>
Subject: Re: Phosphatase enzymatic assay
Phos-tag gels are an option (albeit a fiddly one).
Cheers,
Pat Loll
___________________________
Patrick J. Loll, PhD (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St.
Philadelphia, PA 19102-1192 USA
(267) 359-2653
pj...@drexel.edu
> On 15 Sep 2021, at 8:28 AM, Andrea Moretti <andrea.more...@unige.ch> wrote:
>
> Dear CCP4 community,
>
> sorry for the off topic question but I am struggling with enzymatic assays
> and I would need your help.
>
> I am trying to measure dephosphorylation of a phosphorylated kinase by a
> ser/thr phosphatase. So far I tried to measure it by malachite green assay,
> anti pSer/pThr antibody and PNPase coupled assay but nothing really worked
> for me. NMR is unfortunately not an option since I can't make enough of the
> proteins.
>
> So any hints on phosphatase assays would be helpful.
> Thanks!
>
> Best wishes,
> Andrea
>
>
> --
> Andrea Moretti
> Structural Plant Biology Laboratory
> Department of Botany and Plant Biology
> Sciences III
> University of Geneva
> 30 Quai E. Ansermet
> 1211 Geneva
> Switzerland
> Email: andrea.more...@unige.ch
> Phone: +41 22 379 3029 (office)
> web:http://structplantbio.org
>
> ########################################################################
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
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pjl...@gmail.com
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------------------------------
Date: Wed, 15 Sep 2021 15:26:43 +0000
From: "Hughes, Jonathan" <jon.hug...@bot3.bio.uni-giessen.de>
Subject: AW: Phosphatase enzymatic assay
hey,
my information is that detecting phosphorylation via ms is non-trivial because
the P groups are lost during fragmentation and prior to detection.
cheers
jon
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Wim Burmeister
Gesendet: Mittwoch, 15. September 2021 14:47
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Phosphatase enzymatic assay
Hello,
try mass spectrometry, either after tryptic digestion into peptides or
electrospray MS on the entire protein if it is not too big.
Best
Wim
----- Mail original -----
De: "Andrea Moretti" <andrea.more...@unige.ch>
À: "CCP4BB" <CCP4BB@JISCMAIL.AC.UK>
Envoyé: Mercredi 15 Septembre 2021 14:28:45
Objet: [ccp4bb] Phosphatase enzymatic assay
Dear CCP4 community,
sorry for the off topic question but I am struggling with enzymatic assays and
I would need your help.
I am trying to measure dephosphorylation of a phosphorylated kinase by a
ser/thr phosphatase. So far I tried to measure it by malachite green assay,
anti pSer/pThr antibody and PNPase coupled assay but nothing really worked for
me. NMR is unfortunately not an option since I can't make enough of the
proteins.
So any hints on phosphatase assays would be helpful.
Thanks!
Best wishes,
Andrea
--
Andrea Moretti
Structural Plant Biology Laboratory
Department of Botany and Plant Biology
Sciences III
University of Geneva
30 Quai E. Ansermet
1211 Geneva
Switzerland
Email: andrea.more...@unige.ch
Phone: +41 22 379 3029 (office)
web:http://structplantbio.org
########################################################################
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--
Wim Burmeister
Professor
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs / CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: [ mailto:wim.burmeis...@ibs.fr | wim.burmeis...@ibs.fr ]
Mobile: +33 (0) 7 50 49 19 91
[
http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/
| website ]
Changement climatique : «Les autres combats n’ont aucun sens si celui-là est
perdu» ( Aurélien Barrau )
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------------------------------
Date: Wed, 15 Sep 2021 17:35:06 +0200
From: Mirek Gilski <mi...@amu.edu.pl>
Subject: MX-RDR - Macromolecular Xtallography Raw Data Repository
Dear CCP4 community,
I would like to draw your attention to the Macromolecular Xtallography
Raw Data Repository (MX-RDR). The repository, supported by EU funded
Operational Programme Digital Poland, was created by the
Interdisciplinary Center for Mathematical and Computational Modelling of
University of Warsaw (ICM UW) and the Department of Crystallography of
Adam Mickiewicz University in Poznan.
The MX-RDR repository, accessible via website at
https://mxrdr.icm.edu.pl, was designed as a dedicated archive to provide
access to raw diffraction data collected for macromolecular crystals. It
includes tools for creating sets of crystallographic metadata by
combining information extracted directly from diffraction images and
obtained from a PDB deposit and/or user input. Each data set is
characterized by rich metadata, both to facilitate their management and
long-term curation, and to allow effective scientific reuse. The
resource can be filtered using various criteria and all data are
available for unrestricted access and download.
The experimental data deposited in the repository, in the form of raw
diffraction images and metadata, are stored on ICM UW servers with the
highest standards of protection against their loss.
The key features of the MX-RDR repository include:
1. Persistent identifiers. All data sets receive a persistent and
unique DOI identifier that makes it easy to find and cite them.
2. Versioning. Possibility of placing the next, corrected or
supplemented version of the data set.
3. Embargo. Possibility to set a period during which research data
will not be made available to the public.
4. API (Application Programming Interface). Ability to prepare
scripts that use internal API functions.
I encourage everyone to visit our repository at https://mxrdr.icm.edu.pl
and upload (or download) the raw diffraction data. In case of any
questions, please contact me directly (mi...@amu.edu.pl).
Best regards,
Miroslaw Gilski
MX-RDR Project Leader
Department of Crystallography, Faculty of Chemistry, AMU
& Center for Biocrystallographic Research, IBCh PAS
Poznan, Poland
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------------------------------
Date: Wed, 15 Sep 2021 09:02:05 -0700
From: George Wisedchaisri <gora...@uw.edu>
Subject: Postdoctoral Research Opportunity in Cryo-EM at University of
Washington, in Seattle, USA
Hi,
I have a job opening announcement for a joint postdoctoral position in the
Catterall and Zheng Labs at University of Washington, in Seattle, WA, USA.
Please see attached for more info.
Thanks,
George Wisedchaisri
--
*Postdoctoral Research Position*
*Senior Fellow or Instructor Appointment Level*
*Structural Basis for Function and Pharmacology of Voltage Gated Sodium and
Calcium Channels*
*Laboratories of William A. Catterall and Ning Zheng*
*Department of Pharmacology, University of Washington, Seattle, WA
98195-7280 USA*
*Please respond by e-mail to wcatt...@uw.edu <wcatt...@uw.edu> with
Postdoctoral Application on the Subject Line*
*Position Requirements*
PhD or equivalent in biochemistry, biophysics, bioengineering,
or structural biology.
Experience in molecular biology, cell culture, and protein
expression, purification, and characterization.
Excellent communication skills and successful experience in a team
research environment.
Two years experience with cryo-EM data collection, processing,
and analysis.
Successful determination of a protein structure by cryo-EM.
*Application Requirements*
Curriculum Vitae
Names of three referees
*University of Washington is an affirmative action, equal opportunity
employer. All qualified applicants will receive consideration without
regard to race, color, religion, sex, sexual orientation, gender identity,
gender expression, national origin, age, protected veteran or disabled
status, or genetic information.*
--
George Wisedchaisri, Ph.D.
Research Assistant Professor of Pharmacology
---------------------------------------------
University of Washington School of Medicine
Department of Pharmacology
1959 NE Pacific St
Seattle, WA 98195-7280
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End of CCP4BB Digest - 14 Sep 2021 to 15 Sep 2021 - Special issue (#2021-265)
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