Re: [ccp4bb] peroxy-glutamate?

[Keller, Jacob]

Damage-Selective (DamSel) map?

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bellini, 
Dom
Sent: Wednesday, May 03, 2017 6:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] peroxy-glutamate?


or RDM (raddam detection map), better known as raddamap? :)



BW,



D


From: CCP4 bulletin board > 
on behalf of Pavel Afonine >
Sent: 03 May 2017 22:51:48
To: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] peroxy-glutamate?

Dear Gerard,

I am sure others
are certain to propose a cooler name for that very same type of map
some day ;-) .

a free tip: how about DDM (Decarboxylation Detector Map)?

All the best,
Pavel

Re: [ccp4bb] peroxy-glutamate?

[Pavel Afonine]

Dear Gerard,

I am sure others
> are certain to propose a cooler name for that very same type of map
> some day ;-) .
>

a free tip: how about DDM (Decarboxylation Detector Map)?

All the best,
Pavel

Re: [ccp4bb] peroxy-glutamate?

[Gerard Bricogne]

Dear Ed,

 Thank you for the picture. The decarboxylation of GLU and ASP
side-chains is perhaps the most ubiquitous manifestation of radiation
damage. We have introduced a feature in our autoPROC processing
package whereby, if redundancy in the unmerged data is sufficient to
allow reasonably complete and non-overlapping "early" and "late"
data(sub)sets to be defined, we output "early-minus-late" difference
coefficients that can later be picked up by autoBUSTER to compute the
corresponding difference map. This is a great way of pin-pointing
acidic side-chains, and also sulphur-containing ones. I am sure others
are certain to propose a cooler name for that very same type of map
some day ;-) .

 Here, you seem to have a clear case of partial decarboxylation.
You could try reprocessing your images with autoPROC and computing an
early-minus-late map, just to see what it looks like. If your dataset
complies with the modern low-transmission, high-redundancy paradigm,
it should be very straightforward. You are welcome to get in touch
off-list about this.


 With best wishes,
 
  Gerard.

--
On Wed, May 03, 2017 at 05:19:25PM -0400, Edward A. Berry wrote:
> 
> 
> On 05/03/2017 02:46 PM, Gerard Bricogne wrote:
> >Dear Ed,
> >
> >  Have you considered the possibility that it could be a water
> >stepping in to fill the void created by partial decarboxylation of the
> >glutamate? That could be easily modelled, refined, and tested for its
> >ability to flatten the difference map.
> >
> >  Gerard.
> >
> Actually some of them do appear decarboxylated. Is that something that can 
> happen? In the crystal, or as radiation damage?
> However when there is density for the carboxylate (figure), it appears 
> continuous and linear, doesn't break up into spheres at H-bonding distance - 
> almost like the CO2 is still sitting there- but I guess it would get hydrated 
> to bicarbonate. I could use azide. Or maybe waters with some disorder.
> Thanks,
> eab
> 
> Figure- 2mFo-DFc at 1.3 sigma, mFo-DFc at 3 sigma, green CO2 is shown for 
> comparison, not part of the model.
> 

[ccp4bb] POSTDOCTORAL FELLOWSHIP POSITIONS AVAILABLE - CASE WESTERN RESERVE UNIVERSITY

[Rajesh Ramachandran]

*POSTDOCTORAL POSITIONS AVAILABLE – CASE WESTERN RESERVE UNIVERSITY *

*STRUCTURAL BIOLOGY OF MEMBRANE REMODELING*



Two NIH-funded postdoctoral positions are available immediately in the
Ramachandran Lab at Case Western Reserve University (CWRU) to study the
structural aspects of protein-mediated membrane remodeling during endocytic
and mitochondrial membrane fission. These positions involve intensive
collaboration with the labs of Jason Mears (cryo-EM, CWRU), Matthias Buck
(NMR, CWRU), and Patrick van der Wel (ssNMR, University of Pittsburgh), and
will also entail X-ray crystallography.  The positions require a Ph.D. in
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biophysical techniques to explore protein function on a model membrane
surface. The Ramachandran laboratory also employs a host of cutting-edge
spectroscopic approaches including FRET, fluorescence correlation
spectroscopy (FCS) and fluorescence lifetime imaging (FLIM) to explore
protein-protein and protein-membrane interactions in membrane remodeling
and fission, both *in vitro* and *in vivo*. The Ramachandran lab and the
facilities at CWRU are equipped with state-of-the-art instrumentation for
both biophysical techniques and structural biology, as well as for protein
purification, characterization and membrane reconstitution.

*Requirements*: Applicants must be highly motivated and must have
demonstrated experience (i.e. relevant publications) in protein
biochemistry and structural biology. The candidate should have a strong
conceptual and experimental background in biochemistry and biophysics, as
well as in the mechanistic dissection of structure-function relationships
in proteins; he/she should be independent, proactive, hardworking and
productive; only candidates that have first-author publications (or
articles in press) will be considered. Candidates must have completed their
PhD at the time of appointment. Salary will commensurate with experience
and will adhere to current NIH guidelines. Interested candidates should
submit their CV, reprints of selected publications, three reference letters
(directly from referees), and a cover letter summarizing their experience,
long-term goals, and estimated start date directly to Rajesh Ramachandran
at rxr...@case.edu.

*Relevant Publications. *Please visit our webpage at
*https://physiology.case.edu/people/faculty/rajesh-ramachandran/*



-- 
*Rajesh Ramachandran, Ph.D.,*
*Assistant Professor,*
*E-511, Robbins Bldg., *
*Case Western Reserve University School of Medicine,*
*Cleveland, OH 44106-4970*
*Tel: 1-216-368-2513*

Re: [ccp4bb] peroxy-glutamate?

[Edward A. Berry]

On 05/03/2017 02:46 PM, Gerard Bricogne wrote:

Dear Ed,

  Have you considered the possibility that it could be a water
stepping in to fill the void created by partial decarboxylation of the
glutamate? That could be easily modelled, refined, and tested for its
ability to flatten the difference map.

  Gerard.


Actually some of them do appear decarboxylated. Is that something that can 
happen? In the crystal, or as radiation damage?
However when there is density for the carboxylate (figure), it appears 
continuous and linear, doesn't break up into spheres at H-bonding distance - 
almost like the CO2 is still sitting there- but I guess it would get hydrated 
to bicarbonate. I could use azide. Or maybe waters with some disorder.
Thanks,
eab

Figure- 2mFo-DFc at 1.3 sigma, mFo-DFc at 3 sigma, green CO2 is shown for 
comparison, not part of the model.

Re: [ccp4bb] peroxy-glutamate?

[Gerard Bricogne]

Dear Ed,

 Have you considered the possibility that it could be a water
stepping in to fill the void created by partial decarboxylation of the
glutamate? That could be easily modelled, refined, and tested for its
ability to flatten the difference map.

 Gerard.

--
On Wed, May 03, 2017 at 02:29:11PM -0400, Edward A. Berry wrote:
> Thanks to all who replied. Yes, in some of the other cases density between Cd 
> and Cg is conspicuously weak. From preliminary tests it looks like dual 
> conformations, in some cases together with correlated waters, will account 
> for the density adequately. No Zebras here!
> eab
> 
> On 05/03/2017 04:26 AM, Matthew Merski wrote:
> >Have you tried just a double conformation of the Glu?  Its hard to tell in 
> >your pictures but it looks like there might be less than perfect density for 
> >the CG-CD bond?  If you just try adding a second conf of the Glu that might 
> >work too (and perhaps be a horse rather than a zebra making your hoofprints?)
> >
> >Matthew Merski
> >Crystallochemistry Laboratory
> >Univ. of Warsaw
> >
> >On Wed, May 3, 2017 at 6:29 AM, Edward A. Berry  >> wrote:
> >
> >I'm finishing up refinement of a 1.8A structure (R's 0.17, 0.20) , and 
> > among the largest peaks in the difference map are small spherical blobs 
> > that seem to be attached (1.46 A here) to carboxylate O's (Figures). Are 
> > these likely artifacts? If not, how can I interpret/model them? One idea is 
> > that the acid has reacted with peroxide from the PEG to make the 
> > (hydro)peroxy-acid. I don't know how stable that would be, and I don't see 
> > any peroxyglutamate in Ligand Depot or HIC-Up. Another guess would be acid 
> > hydroxamate but I don't know how that would be generated. Methyl ester 
> > seems to be ruled out by the proximity of the two water molecules (2.45 and 
> > 2.48 A here) suggesting the mystery atom is an H-bond acceptor or donor. 
> > However since the occupancy seems to be < 1, the waters may be there only 
> > when the atom is not.
> >I guess another possibility is there is a lot of motion in the plane of 
> > the carboxylate (up and down here) which cannot be modeled by my isotropic 
> > B-factors. In some cases the green blobs appear on both sides of the 
> > carboxylate (but that could also be alternate conformations of 
> > peroxyglutamate).
> >
> >The difference map (mFo-DFc, green) is contoured at 3 sigma (.06 
> > e-/A^3). The difference peak is 5.4 sigma (0.1 e/A3).
> >The 2mFo-DFc map is contoured at 1.5 sigma (0.1 e/A3). 2mFo-DFc density 
> > extends to the difference peak if I contour down at 0.64 sigma (0.04 e/A3, 
> > third figure).
> >
> >If I put an O atom there, link it with plenty of slack, and refine 
> > occupancy, it goes to 1.54 A from the carboxylate O and refines to 
> > occupancy 0.35, B-factor 15 (carboxylate O is 30). Now it is reached by 
> > 2mFo-DFc density at 1.5 sigma (0.1 e/A3).
> >Any suggestions would be welcome.
> >eab

Re: [ccp4bb] peroxy-glutamate?

[Edward A. Berry]

Thanks to all who replied. Yes, in some of the other cases density between Cd 
and Cg is conspicuously weak. From preliminary tests it looks like dual 
conformations, in some cases together with correlated waters, will account for 
the density adequately. No Zebras here!
eab

On 05/03/2017 04:26 AM, Matthew Merski wrote:

Have you tried just a double conformation of the Glu?  Its hard to tell in your 
pictures but it looks like there might be less than perfect density for the 
CG-CD bond?  If you just try adding a second conf of the Glu that might work 
too (and perhaps be a horse rather than a zebra making your hoofprints?)

Matthew Merski
Crystallochemistry Laboratory
Univ. of Warsaw

On Wed, May 3, 2017 at 6:29 AM, Edward A. Berry > wrote:

I'm finishing up refinement of a 1.8A structure (R's 0.17, 0.20) , and among 
the largest peaks in the difference map are small spherical blobs that seem to be 
attached (1.46 A here) to carboxylate O's (Figures). Are these likely artifacts? 
If not, how can I interpret/model them? One idea is that the acid has reacted with 
peroxide from the PEG to make the (hydro)peroxy-acid. I don't know how stable that 
would be, and I don't see any peroxyglutamate in Ligand Depot or HIC-Up. Another 
guess would be acid hydroxamate but I don't know how that would be generated. 
Methyl ester seems to be ruled out by the proximity of the two water molecules 
(2.45 and 2.48 A here) suggesting the mystery atom is an H-bond acceptor or donor. 
However since the occupancy seems to be < 1, the waters may be there only when 
the atom is not.
I guess another possibility is there is a lot of motion in the plane of the 
carboxylate (up and down here) which cannot be modeled by my isotropic 
B-factors. In some cases the green blobs appear on both sides of the 
carboxylate (but that could also be alternate conformations of peroxyglutamate).

The difference map (mFo-DFc, green) is contoured at 3 sigma (.06 e-/A^3). 
The difference peak is 5.4 sigma (0.1 e/A3).
The 2mFo-DFc map is contoured at 1.5 sigma (0.1 e/A3). 2mFo-DFc density 
extends to the difference peak if I contour down at 0.64 sigma (0.04 e/A3, 
third figure).

If I put an O atom there, link it with plenty of slack, and refine 
occupancy, it goes to 1.54 A from the carboxylate O and refines to occupancy 
0.35, B-factor 15 (carboxylate O is 30). Now it is reached by 2mFo-DFc density 
at 1.5 sigma (0.1 e/A3).
Any suggestions would be welcome.
eab

[ccp4bb] RuH3R system bits and pieces (USA)

[Phil Jeffrey]

I've just started decommissioning our aged Rigaku X-ray system prior to 
replacement and before I consign every bit to surplus and the scrap yard 
there's a possibility that someone else in the USA is nursing an old 
RuH3R/RaxisIV++ system and could find use for a board or TMP controller 
or ...


The only item that might have residual value is the optical upgrade that 
we did 7 years ago - a Xenocs Fox2D Cu 25-25P multilayer.


I have one anode rebuild kit that dates from mid-2013.  I have an 
unopened (but decade+ old) box of filaments (CN4892V2).


Please email me directly, not to the list.

Thanks
Phil Jeffrey
Princeton

[ccp4bb] Research scientist/Lab Manager, Protein Evolution, University of Chicago

[Joseph W Thornton]

Research scientist/Lab manager in Protein Evolution, Thornton Lab, University 
of Chicago

We are seeking an experienced protein biochemist with interest in evolution, 
great experimental and people skills, and strong organizational ability. As a 
senior scientist in the lab, you will conduct independent research on the 
evolution of protein structure and function, help to coordinate the lab’s 
operations, and work closely with students, postdocs, and the PI to develop, 
perform, and interpret experiments and analyses.

A biochemist with expertise in structural biology would be perfect for this 
position. Experience in evolutionary biology is not required, but sincere 
interest in protein evolution is essential.  Our work focuses on the molecular 
and biochemical mechanisms by which ancient proteins evolved their present-day 
functions and physical properties.

The two scientists who have previously held this position in our lab had 
advanced degrees and prior experience as a postdoc or lab manager.  It’s a 
great stable position that allows you to do exciting science and play a key 
role in the lab’s culture.

More information and application instructions can be found at 
http://tiny.cc/Thorntonlabmanager.

More information about the lab is at www.thorntonlab/org.

We are a highly collegial group that draws scientists and students from a 
variety of disciplines – evolution, biochemistry, biophysics, molecular 
biology, computational biology, genetics, and more. The University of Chicago 
is a fantastic place to do science, especially at the interface of evolution 
and the molecular biosciences. Chicago is a great city rich in high and low 
culture; it is also a hipster heaven and, in the summer, a fun beach town.  
People in the lab are fun, funny, interesting, and humane.

Please don’t hesitate to contact me if you have any questions.

Joe Thornton
jo...@uchicago.edu

[ccp4bb] Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing

[Jasmine Young]

On July 12, 2017, the wwPDB partners plan to update the PDB FTP archive 
with PDB structure entry files conforming to V5.0 of the PDBx/mmCIF 
dictionary 
, which 
already supports the global wwPDB system for Deposition, Biocuration, 
and Validation of PDB data - OneDep 
.


In preparation for this update, to allow the community ample time to 
test the planned update and to provide feedback, the wwPDB is now 
delivering PDBx/mmCIF and XML structure entry files for all entries in 
the PDB archive conforming to the new data standards via a new FTP 
repository (ftp://ftp-beta.wwpdb.org/). This collection of test files 
will be updated in concert with regular weekly updates of the PDB archive.


Complete lists of changes can be found at the wwPDB website 
(https://www.wwpdb.org/documentation/remediation).


The wwPDB strongly encourages the community to review and test the 
updated files.


Users should report V5.0 data issues to deposit-h...@mail.wwpdb.org 



We will attempt to address the reported issues incrementally as User 
feedback is received in advance of the rollout on July 12, 2017.


Other derived data and experimental data files of ftp-beta tree will be 
delivered incrementally to the ftp-beta tree between May 3 and July 12, 
2017.


The test FTP area (ftp://ftp.wwpdb.org/pub/pdb/test_data/EM/) containing 
previously updated 3DEM model files (previously made available in 
December 2016) is to be retired effective May 3 2017.





--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

Re: [ccp4bb] ATP analog

[mesters]

Dear Adriana,

this depends on the enzyme i.e. does your enzyme hydrolyse the 
alpha-beta or beta-gamma bond?


If it hydrolyses the beta-gamma bond, options mentioned are indeed:

-AMPPNP (Adenylyl-imidodiphosphate)
-AMPPCP(β,γ-Methyleneadenosine 5′-triphosphate)*
*-AMPPP(S) (ATP-γ-S)
-ADP-BeFx
-ADP-AlFx

Beware though, by replacing the bridging beta-gamma oxygen in ATP to N 
(NH; AMPPNP) or C (CH2; AMPPCP) you loose (O to CH2) the possibility of 
forming or you reverse (O to NH; from acceptor to donor) a hydrogen bond 
here. Thus, the use of the latter two compounds can have adverse effects 
(and you do not want to get into an argument with a referee in the 
future). ATP-γ-S is probably the best option if, bound the the protein, 
hydrolysis is slow enough or the complex crystallizes fast enough (cold 
room!).


ADP-BeFx and ADP-AlFx could be options but again, the charge 
distribution is not equivalent to ATP and it requires additional amino 
acid side chains that coordinate the

AlFx or BeFx group.

Good luck,

Jeroen



Am 02.05.17 um 18:04 schrieb Adriana Sene:

Hi
What are good ATP non hydrolyzable analog for crystallization?

best

Adriana



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than the corresponding NMR structures, including the very best ones. 
Hence, in most cases, a high-resolution crystal structure (< 2.0 Å)will 
provide a better description of the structure in solution than the 
corresponding NMR structure  (Kuszewski, Gronenborn & Clore, 1996, 
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Re: [ccp4bb] ATP analog

[Christian Roth]

Hi,

one word of caution with Metal fluoride complexes. Though they can 
provide valuable inside in the reaction mechanism, even better than some 
ATP-analogues, one has to be careful what metal to use to get the right 
complex.  See review below, which summarises the problems which can 
occur, especially at lower resolution. Also when you have already other 
metals in your crystallisation condition you might not get the complex 
you want to.


Cheers

Christian

DOI:10.1002/anie.201606474 

Am 02.05.2017 um 19:42 schrieb Kevin Jude:
ADP-BeFx and ADP-AlFx (the latter mimics a dissociative transition 
state). The fluoride compounds can be made by mixing BeCl2 or AlCl3 
with excess NaF and then used at say a 3:1 excess over ADP. Be sure to 
dissolve the chloride compounds in a fume hood!


Also ADP-VO4, which can be prepared as described in Goodno CC. Myosin 
active-site trapping with vanadate ion. Meth Enzymol. 1982;85 Pt 
B:116–23.


Best wishes
Kevin

On Tue, May 2, 2017 at 9:04 AM, Adriana Sene > wrote:


Hi
What are good ATP non hydrolyzable analog for crystallization?

best

Adriana




--
Kevin Jude, PhD
Research Specialist, Garcia Lab
Departments of Molecular & Cellular Physiology and Structural Biology
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431 

[ccp4bb] PhD position available at the ALBA synchrotron in Barcelona

[Roeland Boer]

Dear Colleagues

I would really appreciate if you could share the info regarding this 
PhD available in my lab with any potential candidates. It's a 
studentship involving structural biology, protein biochemistry and 
biophysics and microbiology to study conjugation in gram-positive bacteria.


The details on how to apply can be found here:
https://intranet.cells.es/Jobs/JobOffers/ViewJob?job_id=252

In this PhD, you will use a range of molecular biology, genetics, 
biochemistry and structural techniques to understand how the production 
of the conjugational machinery is regulated. The goal is to provide 
insights into the conditions and molecular mechanisms that allow 
conjugation to take place. Subjects of study include the preparation of 
the plasmid DNA for transfer to the donor cell, the cell-to-cell 
communication and regulation of the production of the machinery, as well 
as the transcriptional regulation thereof. The succesful candidate will 
form part of the structural biology group of the XALOC beamline at the 
ALBA synchrotron. The project will be developed in collaboration with 
the group of Wilfried Meijer at the Molecular Biology Center in Madrid 
(CBM - Severo Ochoa, CSIC) and is cofunded by FEDER.


Please direct any inquiries for additional information to rb...@cells.es

Best regards,
Roeland Boer


--

ALBA Synchrotron 

Roeland Boer
BL13-XALOC Beamline Responsible - Experiments Division

ALBA SYNCHROTRON LIGHT SOURCE
Carrer de la Llum 2-26 | 08290 | Cerdanyola del Vallès| Barcelona | 
Spain 

(+34) 93 592 4333 | Beamline (+34) 93 592 4013
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[ccp4bb] Postdoctoral Position in Structural Biology at Case Western Reserve University

[Sudha Chakrapani]

*Postdoctoral Position in Structural Biology at Case Western Reserve
University*



An NIH-funded postdoctoral position is available for a highly motivated
membrane-protein structural biologist in the laboratory of Sudha Chakrapani
at the Department of Physiology and Biophysics, Case Western Reserve
University. The project involves determination of protein structure and the
basis for functional modulation of clinically important ion channels and
transporters (Reference: Basak et. al. *eLife* (2017). We are using
multidisciplinary state-of-the-art approaches to determine structure (X-ray
crystallography and cryo-EM), protein dynamics (EPR and Fluorescence
spectroscopy), and function (patching clamping in proteoliposomes and HEK
cells, two electrode voltage-clamp). We are seeking candidates with a
strong background in molecular biology, membrane protein
expression/purification, and X-ray crystallography. Interested candidates
should email Sudha Chakrapani (sxc...@case.edu) with a cover letter describing
the candidate's research interests, CV, and contact details of three
referees.





Sudha Chakrapani, PhD

Assistant Professor

Department of Physiology and Biophysics

Case Western Reserve University

Robbins Building E-621

Office: (216) 368- <%28216%29%20368-8732>3875

Lab:(216) 368- <%28216%29%20368-3875>8732

Fax:(216) 368-3952, -5586

[ccp4bb] Joint CCP-EM & CCP-BioSim Workshop on EM & MD @University of Leeds

[Tom Burnley]

We are proud to announce a pair of workshops held at the University of
Leeds exploring the crossover between EM and MD.

http://www.ccpem.ac.uk/training/leeds_em_md_2017/leeds_em_md.php

(1) Computation for Biomolecular Cryo-Electron Microscopy and Tomography
Sarah Harris (CCP-BioSim/Physics, Leeds), Albert Solernou (Physics/Leeds)
and Ste Muench (Biological Sciences, Leeds), Tom Burnley (CCP-EM/STFC)

CCPBioSim-EM Workshop (14th July): Structural characterisation of proteins
and protein complexes by cryo-EM and cryo-ET is now providing access to a
wide range of macromolecular assemblies that were inaccessible by X-ray
crystallography or NMR. Although EM analysis can provide information on
different conformational states, it is still an averaging technique and
therefore highly dynamic regions can be difficult to resolve. This workshop
will explore the emerging computational techniques for achieving biological
understanding from cryo-EM/ET images, and discuss areas most in need of
further development.  Confirmed speakers include:

Christiane Berger-Schaffitzel, University of Bristol
Christian Blau (Lindahl Group, Stockholm University)
Max Bonomi (Vendruscolo Group), Univeristy of Cambridge
Tom Burnley, CCP-EM / STFC
Jose-Maria Carazo, National Center for Biotechnology, Spain
Tristan Croll, Univeristy of Cambridge
Sarah Harris, University of Leeds
Agnel Joseph (Topf Group), Birkbeck
Elena Orlova, Birkbeck

Registration:
https://eventbooking.stfc.ac.uk/news-events/computation-for-biomolecular-cryo-electron-microscopy-and-tomography-workshop-380

(2) FFEA Workshop (13th July): This will be a hands-on workshop on the new
software tool Fluctuating Finite Element Analysis (FFEA), which calculates
dynamic trajectories for flexible biomolecules directly from cryo-EM/ET
density maps. FFEA aims to provide an equivalent simulation tool for the
EMDB as atomistic MD simulations have for the PDB. This approach uniquely
uses volumetric meshes rather than atomistic co-ordinates as input such
that it can model protein dynamics, protein-protein interactions,
conformational switching between known configurational states and can be
mapped back to atomistic co-ordinates, where these are available. This
workshop is ideal for biomolecular simulators who would like to make full
use of cryo-EM data in their modelling, or for experimentalists who would
like to gain new theoretical insight into the dynamic behaviour of the
structures they observe.

Registration:
https://eventbooking.stfc.ac.uk/news-events/ffea-practical-workshop-381

Best wishes,

Tom

-- 
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

Re: [ccp4bb] HETATM record after Refmac

[Jan Stransky]

Indeed, even from i2. The issue is somewhere else, sorry for blaming refmac.
Jan

On 05/03/2017 01:09 PM, Robbie Joosten wrote:

Hi Jan,

That could be a postprocessing thing, because that version of Refmac works fine 
from the command line or from CCP4i (at least in my hands on Linux).

Cheers,
Robbie


-Original Message-
From: Jan Stransky [mailto:jan.stransky.c...@gmail.com]
Sent: Wednesday, May 03, 2017 13:05
To: Robbie Joosten
Subject: Re: [ccp4bb] HETATM record after Refmac

Dear Robbie,
It is refmac from current CCP4 release. It is run from i2.
This is in the log: CCP4 7.0.036: Refmac  version 5.8.0158 :
03/10/16
Jan

On 05/03/2017 12:53 PM, Robbie Joosten wrote:

Dear Jan,

That problem was solved many versions ago. Which version of REFMAC are

you using? Is there perhaps another program handling the files before they
go to COOT?

Cheers,
Robbie


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf

Of

Jan Stransky
Sent: Wednesday, May 03, 2017 10:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] HETATM record after Refmac

Dear ccp4ers,

is there way to retain HETATM keyword for ligands when running refmac?
It apparently changes HETATM to ATOM which spoils some nice ligand
features in Coot...

Best regards,

Jan

Re: [ccp4bb] ATP analog

[Adriana Sene]

Thanks every one for the great help. I am loaded with all the useful
information.

best
 Adriana

On Tue, May 2, 2017 at 9:07 PM, Deaconescu, Alexandra <
alexandra_deacone...@brown.edu> wrote:

> Hi,
>
> ATPgS is an option, but it is slowly hydrolysable, so depending on your
> enzyme, it might not be the best one to use.
>
> Cheers,
> Alexandra
>
>
> On Tue, May 2, 2017 at 2:56 PM, Aaron Thompson  > wrote:
>
>> ATP-gamma-S is another option.  There are 123 public structures
>> containing this ligand (ligand ID AGS).
>>
>>
>> Cheers,
>>
>>
>> Aaron
>>
>> On Tue, May 2, 2017 at 11:42 AM, Kevin Jude  wrote:
>>
>>> ADP-BeFx and ADP-AlFx (the latter mimics a dissociative transition
>>> state). The fluoride compounds can be made by mixing BeCl2 or AlCl3 with
>>> excess NaF and then used at say a 3:1 excess over ADP. Be sure to dissolve
>>> the chloride compounds in a fume hood!
>>>
>>> Also ADP-VO4, which can be prepared as described in Goodno CC. Myosin
>>> active-site trapping with vanadate ion. Meth Enzymol. 1982;85 Pt B:116–23.
>>>
>>> Best wishes
>>> Kevin
>>>
>>> On Tue, May 2, 2017 at 9:04 AM, Adriana Sene 
>>> wrote:
>>>
 Hi
 What are good ATP non hydrolyzable analog for crystallization?

 best

 Adriana

>>>
>>>
>>>
>>> --
>>> Kevin Jude, PhD
>>> Research Specialist, Garcia Lab
>>> Departments of Molecular & Cellular Physiology and Structural Biology
>>> Stanford University School of Medicine
>>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>>> Phone: (650) 723-6431
>>>
>>
>>
>

[ccp4bb] HETATM record after Refmac

[Jan Stransky]

Dear ccp4ers,

is there way to retain HETATM keyword for ligands when running refmac? 
It apparently changes HETATM to ATOM which spoils some nice ligand 
features in Coot...


Best regards,

Jan

Re: [ccp4bb] peroxy-glutamate?

[Tristan Croll]

Peroxyacids are unlikely - they're very reactive/unstable under normal 
conditions. Is it possible your crystal is just at unusually low pH so these 
acids are protonated? That makes the carbon-oxygen bond lengths asymmetric, 
possibly by enough to explain your blobs.

Tristan

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 3 May 2017, at 05:29, Edward A. Berry  wrote:
> 
> I'm finishing up refinement of a 1.8A structure (R's 0.17, 0.20) , and among 
> the largest peaks in the difference map are small spherical blobs that seem 
> to be attached (1.46 A here) to carboxylate O's (Figures). Are these likely 
> artifacts? If not, how can I interpret/model them? One idea is that the acid 
> has reacted with peroxide from the PEG to make the (hydro)peroxy-acid. I 
> don't know how stable that would be, and I don't see any peroxyglutamate in 
> Ligand Depot or HIC-Up. Another guess would be acid hydroxamate but I don't 
> know how that would be generated. Methyl ester seems to be ruled out by the 
> proximity of the two water molecules (2.45 and 2.48 A here) suggesting the 
> mystery atom is an H-bond acceptor or donor. However since the occupancy 
> seems to be < 1, the waters may be there only when the atom is not.
> I guess another possibility is there is a lot of motion in the plane of the 
> carboxylate (up and down here) which cannot be modeled by my isotropic 
> B-factors. In some cases the green blobs appear on both sides of the 
> carboxylate (but that could also be alternate conformations of 
> peroxyglutamate).
> 
> The difference map (mFo-DFc, green) is contoured at 3 sigma (.06 e-/A^3). The 
> difference peak is 5.4 sigma (0.1 e/A3).
> The 2mFo-DFc map is contoured at 1.5 sigma (0.1 e/A3). 2mFo-DFc density 
> extends to the difference peak if I contour down at 0.64 sigma (0.04 e/A3, 
> third figure).
> 
> If I put an O atom there, link it with plenty of slack, and refine occupancy, 
> it goes to 1.54 A from the carboxylate O and refines to occupancy 0.35, 
> B-factor 15 (carboxylate O is 30). Now it is reached by 2mFo-DFc density at 
> 1.5 sigma (0.1 e/A3).
> Any suggestions would be welcome.
> eab
> 
> 
>