Re: [ccp4bb] Coot for Fedora Core 3

[Kay Diederichs]

Vellieux Frederic schrieb:

Dear All,

Would anyone know where to find the latest stable release of Coot for 
Fedora Core 3? I tried to access the pages ~emsley on the York ysbl 
server, but to no avail (You don't have permission to access 
/~emsley/coot/ on this server.).


Thank you in advance,

Fred.


Fred,

latest stable version for FC3 should be 
coot-0.4.1-binary-Linux-i386-redhat-8.0.tar.gz which can be found at 
ftp://turn5.biologie.uni-konstanz.de/coot/  (this is updated nightly 
from ysbl)


HTH,

Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz


smime.p7s
Description: S/MIME Cryptographic Signature

[ccp4bb] Coot for Fedora Core 3

[Vellieux Frederic]

Dear All,

Would anyone know where to find the latest stable release of Coot for 
Fedora Core 3? I tried to access the pages ~emsley on the York ysbl 
server, but to no avail (You don't have permission to access 
/~emsley/coot/ on this server.).


Thank you in advance,

Fred.
begin:vcard
fn:Fred. Vellieux (Ph.D)
n:Vellieux (Ph.D);Fred.
email;internet:[EMAIL PROTECTED]
tel;work:+33 438789605
version:2.1
end:vcard

[ccp4bb] Oxidized manganese?

[TC Hu]

Dear all,

Sorry for the non-topic question. We are working on an enzyme with two Mn2+
in its active center. The Mn2+-coordinated water molecules are responsible
for binding and nucleophillic attack of the substrate. We soaked the protein
crystal with an inhibitor and determined the structure, in which we did not
find the inhibitor. However, from the Fsoaked_crystal - Funsoaked_crystal
map constructed with the refined phases, we discovered two strong (>4 sigma)
difference signal near the two Mn2+, one for each. Both two datasets were
collected to 2.2A and of good quality. Considering the strong effect of the
inhibitor (IC50 ~75nM), we doubt that the manganese ions might be oxidized
and the catalytic water molecules are replaced. But since there are several
oxidation states of manganese, how can we verify which one occurred in our
crystal?

Another minor question: is there any movie-making software that can produce
the animation of bond formation and breakage (like that during catalysis)?

Thanks for your input!

Tiancen Hu
Shanghai Institute of Materia Medica
Chinese Academy of Sciences

[ccp4bb] dry shipper on airplaine

[Clemens Grimm]

Dear all,

I wonder if it would be still/again possible to check in a dry shipper for a
flight inside Europe. What is your experience?

Cheers,
Clemens

[ccp4bb] Job offer: Protein Crystallographer (with Ph.D)

[Blaesse, Michael]

PROTEROS is a leading service-provider for the preparation and
three-dimensional structural analysis of proteins for structure-guided
drug discovery. Our work contributes to fast and rational development of
new therapeutic compounds. Since its foundation in 1998, PROTEROS is a
continuously growing, renowned enterprise collaborating with a large
variety of international Pharma, Biotech and Crop Science companies.

To support our existing crystallography team we are looking for a

Protein Crystallographer (female/male)

 

Job description

You will be responsible for

- planning and execution of protein crystallization experiments

- accomplishment of small molecule ligand binding to protein crystals

- analysis and evaluation of protein crystallization experiments,
protein crystals, and protein X-ray diffraction patterns

- evaluation of protein X-ray diffraction data

- X-ray diffraction data collection at in-house generators and
synchrotron beamlines

- further development and optimization of methods and work-flows in
protein crystallization and protein crystal structure determination

- protein structure solution, modelling and refinement

 

The successful candidate will meet the following requirements

You have a Ph.D. in Chemistry, Biology, or Pharmacy with excellent
records providing you with a profound knowledge and experience in
protein crystallization, protein-ligand crystal complex formation and
protein structure determination. Knowledge and experience in
Fragment-based crystallography would be a plus. A good knowledge with
personal computers including UNIX/LINUX systems and acquaintance with
current software packages employed in protein crystallography are
mandatory.

You are proactive and able to work effectively under strict time lines.

Additionally, you have excellent communication skills and like to work
in a multi-disciplinary team. Industry experience in the life science
industry is an asset.

 

Please apply by sending your full application documents to

bewerbung at proteros.de

or to

Rabea Neumann | Am Klopferspitz 19 | 82152 Martinsried | Germany

 

 

Re: [ccp4bb] Oxidized manganese?

[Klaus Piontek]

Dear Tiancen,

I would look to the coordination of the Mn. In other words to the 
geometry and distances from the Mn to it's potential ligands. The most 
stable oxidation state of Mn is +2, with a octahedral (6-fold) 
coordination sphere and bond lengths (e.g. Mn-O) of 2.1-2.4 Å. For Mn3+ 
one would expect somewhat longer bonds. But Mn3+ is probably not stable 
in the environment of a protein. Even if the Mn2+ was oxidized and 
stayed like that, during data collection (at least at a high dose like 
at a synchrotron) one could expect reduction through X-ray radiation.



Greetings,

Klaus

TC Hu wrote:

Dear all,

Sorry for the non-topic question. We are working on an enzyme with two Mn2+
in its active center. The Mn2+-coordinated water molecules are responsible
for binding and nucleophillic attack of the substrate. We soaked the protein
crystal with an inhibitor and determined the structure, in which we did not
find the inhibitor. However, from the Fsoaked_crystal - Funsoaked_crystal
map constructed with the refined phases, we discovered two strong (>4 sigma)
difference signal near the two Mn2+, one for each. Both two datasets were
collected to 2.2A and of good quality. Considering the strong effect of the
inhibitor (IC50 ~75nM), we doubt that the manganese ions might be oxidized
and the catalytic water molecules are replaced. But since there are several
oxidation states of manganese, how can we verify which one occurred in our
crystal?

Another minor question: is there any movie-making software that can produce
the animation of bond formation and breakage (like that during catalysis)?

Thanks for your input!

Tiancen Hu
Shanghai Institute of Materia Medica
Chinese Academy of Sciences

  



--
Dr. Klaus Piontek
Albert-Ludwigs-University Freiburg
Institute of Organic Chemistry and Biochemistry, Room 401 H 
Albertstrasse 21
D-79104 Freiburg 
Germany

Phone: ++49-761-203-6036
Fax: ++49-761-203-8714
Email: [EMAIL PROTECTED]
Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/

Re: [ccp4bb] dry shipper on airplaine

[Ronnie Berntsson]

In my experience it is still possible to do so, but that rather  
depends from where you are flying. From my own experience it is always  
good to contact the airport in question well in advance, partly to  
check with them that it is ok, partly to let them know when you intend  
to fly. This tends to work well with airports in Sweden, but less well  
in other countries. I know of one occasion when a dewar was stopped on  
Schiphol, Netherlands, even though it had gone through security (the  
captain of the airplane said no..). Bringing it back home from ESRF  
(eg flying from Lyon) rarely poses any trouble, they seem to be used  
to dewars.


Cheers,
Ronnie


On May 27, 2008, at 2:28 PM, Clemens Grimm wrote:


Dear all,

I wonder if it would be still/again possible to check in a dry  
shipper for a

flight inside Europe. What is your experience?

Cheers,
Clemens

[ccp4bb] CCP4 at the ACA in Knoxville

[Keegan, RM (Ronan)]

Dear All,

This year's  ACA is nearly upon us and CCP4 will again be running a
stand at the exhibition. Please come along to the stand where Francois
and myself will be there to answer any questions you may have about the
suite and demonstrate some of the new features in the upcoming CCP4 6.1
release.

We look forward to seeing you in Knoxville.

Best wishes,

Ronan

   

[ccp4bb] Problem with crystallization of Se-Met labeled protein

[Joe Smith]

Dear all,
Sorry for an off-topic query.
I have been unable to crystallize a Se-met containing protein (8 Met
in 206 amino acids) in the native crystallization condition ( 0.1 M
Tris pH 8.5, 1.2 M K-Na-tartrate; Theoretical pI of protein is 8.4).
As expected, solubility of Se-Met containing protein is little less
than the wild type. Other than seeding, i don't know what else I
should try for obtaining a Se-met crystal for phasing. Can I mutate
some of the exposed Met  (based on secondary structure prediction and
homologous structure) to Ala as I feel I don't really need 8 Se for
phasing 208 aa long polypeptide. I want to know what generally one
should do when Se-Met containing proteins fail to crystallize.
Thanks in advance.
Joe
PS: Since, protein contains 3 Cys residues.. I am also planning to try
my luck with heavy atom compounds containing Hg.

Re: [ccp4bb] Problem with crystallization of Se-Met labeled protein

[Jim Pflugrath]

Have you thought about phasing off the sulfurs?  This is quite a common 
technique nowadays.


Jim

On Tue, 27 May 2008, Joe Smith wrote:


Dear all,
Sorry for an off-topic query.
I have been unable to crystallize a Se-met containing protein (8 Met
in 206 amino acids) in the native crystallization condition ( 0.1 M
Tris pH 8.5, 1.2 M K-Na-tartrate; Theoretical pI of protein is 8.4).
As expected, solubility of Se-Met containing protein is little less
than the wild type. Other than seeding, i don't know what else I
should try for obtaining a Se-met crystal for phasing. Can I mutate
some of the exposed Met  (based on secondary structure prediction and
homologous structure) to Ala as I feel I don't really need 8 Se for
phasing 208 aa long polypeptide. I want to know what generally one
should do when Se-Met containing proteins fail to crystallize.
Thanks in advance.
Joe
PS: Since, protein contains 3 Cys residues.. I am also planning to try
my luck with heavy atom compounds containing Hg.

Re: [ccp4bb] Problem with crystallization of Se-Met labeled protein

[Artem Evdokimov]

Hi,

Unless you've already tried exhaustively - why not to try MIR, as you
mentioned - there are many derivatives out there to be tried and with a
small protein the chances are pretty good. All you need is one good
derivative :)

This certainly sounds easier than mutating exposed Met!

Cross-seeding with S-Met crystals into Se-Met protein worked for me on
several occasions.

Artem

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joe
Smith
Sent: Tuesday, May 27, 2008 5:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with crystallization of Se-Met labeled protein

Dear all,
Sorry for an off-topic query.
I have been unable to crystallize a Se-met containing protein (8 Met
in 206 amino acids) in the native crystallization condition ( 0.1 M
Tris pH 8.5, 1.2 M K-Na-tartrate; Theoretical pI of protein is 8.4).
As expected, solubility of Se-Met containing protein is little less
than the wild type. Other than seeding, i don't know what else I
should try for obtaining a Se-met crystal for phasing. Can I mutate
some of the exposed Met  (based on secondary structure prediction and
homologous structure) to Ala as I feel I don't really need 8 Se for
phasing 208 aa long polypeptide. I want to know what generally one
should do when Se-Met containing proteins fail to crystallize.
Thanks in advance.
Joe
PS: Since, protein contains 3 Cys residues.. I am also planning to try
my luck with heavy atom compounds containing Hg.

[ccp4bb] Protein biochemistry position available

[Bussiere, Dirksen]

Novartis Oncology in Emeryville is seeking a highly motivated scientist
to contribute with Protein Biochemistry expertise to the pre-clinical
development of targeted oncology therapies.

 

The candidate should have extensive expertise in the area of Protein
purification and characterization. The ideal candidate will have a Ph.D.
in biochemistry or related field, productive post-doctoral work and 3+
years of relevant biopharmaceutical experience. The successful candidate
will apply these skills to produce proteins for X-ray crystallography,
high-throughput screening and therapeutic antibody programs. Candidates
should have a proven track record of developing and optimizing protein
purification processes.  Candidate should have excellent instrument
skills including the use of AKTA systems and HPLC.  Extensive experience
with a wide variety of biochemical methods for protein characterization
(protein quantitation, protein modification strategies, cross linking,
limited proteolysis) is required. Background in mass spectrometry and/or
expertise using techniques such as surface plasmon resonance, light
scattering and fluorescence spectroscopy, is highly desirable.
Experience working on X-ray crystallography teams would be a plus. 

 

The candidate should have excellent people management skills, the
ability to effectively collaborate within multidisciplinary teams, and
very good communication skills. This position will have some reporting
responsibilities but will substantially contribute and lead from the
bench.  

 

To join our global team, please submit your CV online at
http://www.novartisvaccines.com/jobs
  , referencing Brassring
requisition number 2316BR.

 

Dirksen Bussiere, Ph.D., M.B.A.

Computational Chemistry & Structural Chemistry

Novartis Institutes for Biomedical Research 

4560 Horton Street, M/S 4.4

Emeryville, CA.  94608

Phone: 510-923-2114

Fax:  510-923-5550

e-mail:  [EMAIL PROTECTED]

 

 

[ccp4bb] odd waters

[Bernhard Rupp]

Dear All,

something one/some of you might have seen already and 
might know what it might be/how to analyse:

Material: dimer of Se-Met, Ni-purified, NaCl and NaAc in
purification history.

I have 4 'waters', 2 each in the same monomer location
in a dimer of 2.5A Se-Met structure. They are multiple
coordinated - perhaps dist octahedron - and refine down to
B=2.0 and show correspondingly strong density. Surrounding
protein Bs range from 15 backbone to 37 Arg sidechain 

First idea of course metal ions.  
But the distances are odd - 3.1 to 3.7, unusually long for
common metal coordination.

If I use Na+/Mg++, the Bs still refine down to 4 to 6
K+ B's run up to ~25, Ni++ to 35-40, could be partial occ. 

Given the charge distribution I doubt Cl- makes sense -
it sure looks like a nice place for cation. Not enough space
for sul- and fos-fates. 

No experiments possible, have to deal with what's on hand.

Images on web:
http://www.ruppweb.org/images/snap.gif
http://www.ruppweb.org/images/mystery_ion.gif

How common are such large coordination distances in protein/metal 
coordination and are there any (in silico) analysis tools one could use?

Thx, br
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
[EMAIL PROTECTED]
[EMAIL PROTECTED] 
http://www.ruppweb.org/ 
-
The hard part about playing chicken
is to know when to flinch
-

Re: [ccp4bb] Problem with crystallization of Se-Met labeled protein [Fwd: Rejected posting to [EMAIL PROTECTED]

[Jens Kaiser]

Hey Joe,

set up a coarser grid around the native conditions. I know of one case
where semet crystallized nearly 2 full pH units lower than native. A
colleague made a couple of years ago a reasonable suggestion: don't do
s-met at all, do the crystal screening directly with se-met. Nowadays
certainly affordable.

good luck

Jens

On Tue, 2008-05-27 at 17:11 -0400, Joe Smith wrote:
> Dear all,
> Sorry for an off-topic query.
> I have been unable to crystallize a Se-met containing protein (8 Met
> in 206 amino acids) in the native crystallization condition ( 0.1 M
> Tris pH 8.5, 1.2 M K-Na-tartrate; Theoretical pI of protein is 8.4).
> As expected, solubility of Se-Met containing protein is little less
> than the wild type. Other than seeding, i don't know what else I
> should try for obtaining a Se-met crystal for phasing. Can I mutate
> some of the exposed Met  (based on secondary structure prediction and
> homologous structure) to Ala as I feel I don't really need 8 Se for
> phasing 208 aa long polypeptide. I want to know what generally one
> should do when Se-Met containing proteins fail to crystallize.
> Thanks in advance.
> Joe
> PS: Since, protein contains 3 Cys residues.. I am also planning to try
> my luck with heavy atom compounds containing Hg.

Re: [ccp4bb] odd waters

[Abhinav Kumar]

Check the anomalous difference map on these sites.

Thanks
Abhinav

Abhinav Kumar
JCSG @ SSRL, MS 99
2575 Sand Hill Road
Menlo Park, CA 945025-7015

Phone: 650 926 2992
Fax: 650 926 3292



On May 27, 2008, at 6:38 PM, Bernhard Rupp wrote:


Dear All,

something one/some of you might have seen already and
might know what it might be/how to analyse:

Material: dimer of Se-Met, Ni-purified, NaCl and NaAc in
purification history.

I have 4 'waters', 2 each in the same monomer location
in a dimer of 2.5A Se-Met structure. They are multiple
coordinated - perhaps dist octahedron - and refine down to
B=2.0 and show correspondingly strong density. Surrounding
protein Bs range from 15 backbone to 37 Arg sidechain

First idea of course metal ions.
But the distances are odd - 3.1 to 3.7, unusually long for
common metal coordination.

If I use Na+/Mg++, the Bs still refine down to 4 to 6
K+ B's run up to ~25, Ni++ to 35-40, could be partial occ.

Given the charge distribution I doubt Cl- makes sense -
it sure looks like a nice place for cation. Not enough space
for sul- and fos-fates.

No experiments possible, have to deal with what's on hand.

Images on web:
http://www.ruppweb.org/images/snap.gif
http://www.ruppweb.org/images/mystery_ion.gif

How common are such large coordination distances in protein/metal
coordination and are there any (in silico) analysis tools one could  
use?


Thx, br
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
[EMAIL PROTECTED]
[EMAIL PROTECTED]
http://www.ruppweb.org/
-
The hard part about playing chicken
is to know when to flinch
-

[ccp4bb] pattern search in substructure?

[Juergen J. Mueller]

Dear all,
given a very overcrowded substucture (e.g. from SHELX, PnB for sulfur) 
in a big asymmetric unit (over 100 proposed S),

given the resolution used for the substructur determination,
given several possible S-patterns (taken from PDB), like PAN-pattern, 
Apple-pattern a.s.o. as a pdb-file.
Which program can be used to find the given pattern in the substructure 
(NCS search, ...) taking
into account the error limits for the S-atom positions? Automatical 
NCS-search independent of the search pattern (using Solve/Resolve, SnB) 
does not work.

Any hint is welcome,
Juergen

Re: [ccp4bb] pattern search in substructure?

[Clemens Vonrhein]

Hi Juergen,

PROFESSS can be misused (?) to do this:

 - just create a PDB file first the pattern atoms (numbered 1 to N)
   and then the atoms of the substructure (numbered N+1 to M).

 - you can then look for 'NCS' where only (1-N) atoms are related to
   only (N+1-M) atoms.

Just run something like

professs xyzin pattern+substructure.pdb xysout professs.pdb < Dear all,
> given a very overcrowded substucture (e.g. from SHELX, PnB for sulfur) 
> in a big asymmetric unit (over 100 proposed S),
> given the resolution used for the substructur determination,
> given several possible S-patterns (taken from PDB), like PAN-pattern, 
> Apple-pattern a.s.o. as a pdb-file.
> Which program can be used to find the given pattern in the substructure 
> (NCS search, ...) taking
> into account the error limits for the S-atom positions? Automatical 
> NCS-search independent of the search pattern (using Solve/Resolve, SnB) 
> does not work.
> Any hint is welcome,
> Juergen
> 

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] odd waters

[Bernhard Rupp]

Dear All,
 
the consensus is that Cl- is most likely,
given the fact that backbone Ns and Arg 
are involved in the contacts.
 
I think there is something wrong with my 
surface calulation - need to check.

Thx! BR
  _  

From: Petri Kursula [mailto:[EMAIL PROTECTED] 
Sent: Tuesday, May 27, 2008 9:38 PM
To: [EMAIL PROTECTED]
Subject: [Bulk] Re: [ccp4bb] odd waters


>From the coordination environment and distances, sure looks like a chloride
ion. 
Petri

On May 28, 2008, at 4:38 AM, Bernhard Rupp wrote:


Dear All,

something one/some of you might have seen already and 
might know what it might be/how to analyse:

Material: dimer of Se-Met, Ni-purified, NaCl and NaAc in
purification history.

I have 4 'waters', 2 each in the same monomer location
in a dimer of 2.5A Se-Met structure. They are multiple
coordinated - perhaps dist octahedron - and refine down to
B=2.0 and show correspondingly strong density. Surrounding
protein Bs range from 15 backbone to 37 Arg sidechain 

First idea of course metal ions. 
But the distances are odd - 3.1 to 3.7, unusually long for
common metal coordination.

If I use Na+/Mg++, the Bs still refine down to 4 to 6
K+ B's run up to ~25, Ni++ to 35-40, could be partial occ. 

Given the charge distribution I doubt Cl- makes sense -
it sure looks like a nice place for cation. Not enough space
for sul- and fos-fates. 

No experiments possible, have to deal with what's on hand.

Images on web:
http://www.ruppweb.org/images/snap.gif
http://www.ruppweb.org/images/mystery_ion.gif

How common are such large coordination distances in protein/metal 
coordination and are there any (in silico) analysis tools one could use?

Thx, br
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
[EMAIL PROTECTED]
[EMAIL PROTECTED] 
http://www.ruppweb.org/ 
-
The hard part about playing chicken
is to know when to flinch
-



---
Petri Kursula, Ph.D.
Academy Research Fellow
Docent of Neurobiochemistry
Department of Biochemistry
University of Oulu
Oulu, Finland
[EMAIL PROTECTED]
cc.oulu.fi/~pkursula
www.biochem.oulu.fi/kursula
---