Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Eleanor Dodson]

I am serious about checking the anomalous map!!
(trivial from REFMAC - key word anom map on)
Then do a peak search and just check first that the rogue residue IS  CYS
first - you should see the S as a peak..)

Eleanor


On Wed, 10 Jul 2019 at 07:38, Lumbini Yadav  wrote:

> Thanks for the reply.
> The distance between sulphur and centre of   Fo-Fc map is around 2.5A. The
> density does not appear to be of hydrogen (attached image) anisotropy
> refinement also does not help.
>
> On Tue, Jul 9, 2019 at 5:13 PM Anthony Addlagatta 
> wrote:
>
>> Lumbini,
>>
>> It would useful to know the distance between the sulfur and center of the
>> Fo-Fc map that you have shown. Since you have very high resolution data,
>> the extra density could be for a hydrogen atom in CSO-H (sufeneic acid) or
>> anisotropy of the oxygen atom.
>>
>> Anthony
>> --
>> *From: *176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk
>> *To: *CCP4BB@JISCMAIL.AC.UK
>> *Sent: *Tuesday, July 9, 2019 4:48:32 PM
>> *Subject: *Re: [ccp4bb] Fo-Fc density close to cysteine residue
>>
>> Any anomalous diffraction?
>>
>> On Tue, 9 Jul 2019 at 10:32, Lumbini Yadav  wrote:
>>
>>> Dear all,
>>>
>>>
>>>
>>> We have found a huge Fo-Fc density close to cysteine residue (see
>>> attached image) in the structure with resolution of 1.2A. In the
>>> crystallization condition, we have PEG 3350, Potassium phosphate
>>> monobasic, glycerol and protein was in Tris and NaCl. Before freezing
>>> the crystals were soaked in mother liquor containing sodium dithionite.
>>>
>>>
>>>
>>> I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
>>> CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in
>>> all the screenings we do see some part of Fo-Fc density unaddressed at
>>> 3 sigma.
>>>
>>>
>>>
>>> Does anyone have an idea about what this density could be? Covalent
>>> modification?
>>>
>>>
>>>
>>> Thanks.
>>>
>>>
>>>
>>> Kind regards,
>>>
>>> Lumbini
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>>
>>
>>
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>>
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>
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Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Lumbini Yadav]

Thanks for the reply.
The distance between sulphur and centre of   Fo-Fc map is around 2.5A. The
density does not appear to be of hydrogen (attached image) anisotropy
refinement also does not help.

On Tue, Jul 9, 2019 at 5:13 PM Anthony Addlagatta 
wrote:

> Lumbini,
>
> It would useful to know the distance between the sulfur and center of the
> Fo-Fc map that you have shown. Since you have very high resolution data,
> the extra density could be for a hydrogen atom in CSO-H (sufeneic acid) or
> anisotropy of the oxygen atom.
>
> Anthony
> --
> *From: *176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk
> *To: *CCP4BB@JISCMAIL.AC.UK
> *Sent: *Tuesday, July 9, 2019 4:48:32 PM
> *Subject: *Re: [ccp4bb] Fo-Fc density close to cysteine residue
>
> Any anomalous diffraction?
>
> On Tue, 9 Jul 2019 at 10:32, Lumbini Yadav  wrote:
>
>> Dear all,
>>
>>
>>
>> We have found a huge Fo-Fc density close to cysteine residue (see
>> attached image) in the structure with resolution of 1.2A. In the
>> crystallization condition, we have PEG 3350, Potassium phosphate
>> monobasic, glycerol and protein was in Tris and NaCl. Before freezing
>> the crystals were soaked in mother liquor containing sodium dithionite.
>>
>>
>>
>> I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
>> CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in
>> all the screenings we do see some part of Fo-Fc density unaddressed at 3
>> sigma.
>>
>>
>>
>> Does anyone have an idea about what this density could be? Covalent
>> modification?
>>
>>
>>
>> Thanks.
>>
>>
>>
>> Kind regards,
>>
>> Lumbini
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
>
>
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>
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Re: [ccp4bb] Characterizing a binding pocket

[Duangrudee Tanramluk]

Dear Jessica,

You can try http://manoraa.org for ligand interaction observation. This server 
helps you to observe structural conservation environment of any  ligand in the 
PDB by clicking atoms versus PDB chains you want to superpose on. If you 
classify HEME into different UNIPROT, you can see where the major differences 
in atomic conservation from each set lies. You can also select a partial 
fragment of HEME that you want to characterise the interaction types for each 
ligand-residues partners too. 

Just type in 'HEM' on the three letter code panel of this URLs 

http://manoraa.icbs.mahidol.ac.th/Manoraa/


Best wishes,
Duangrudee

Duangrudee Tanramluk, Ph.D.
Institute of Molecular Biosciences, Mahidol University
Puttamonthon 4 Rd., Salaya, Nakhon Pathom 73170 THAILAND



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[ccp4bb] Research Associate Opening at NE-CAT, at the APS

[Salbego, Cyndi]

The Northeastern Collaborative Access Team (NE-CAT), located at the Advanced 
Photon Source at the Argonne National Laboratory in suburban Chicago, is 
seeking applicants for a beamline scientist position. The primary 
responsibilities of the staff scientist will be to provide user training and 
support using NE-CAT’s X-ray beamlines; assist in setting up experiments; 
provide crystallographic expertise to ensure the highest quality data and 
structures; and contribute to the continued development of software tools.

Duties and Responsibilities:
•   Provide user training and support; both onsite and via remote 
conferencing. This involves work nights and weekends, approximately nine months 
of the year, when the APS has run cycles and is open for data acquisition. 
During these months, the staff scientist will rotate assignments with other 
staff members to provide support 24 hours a day, seven days a week.
•   Test, modify or develop crystallographic software.
•   Test and debug new beamline software and hardware. Evaluate beamline 
performance to produce optimum data. Contribute to the development of beamline 
troubleshooting procedures.
•   Use knowledge of synchrotron beamline optics and experiment-specific 
topics to develop data collection and structure determination procedures.
•   Take part in development of real time data analysis software for the 
beamline data acquisition software RAPD.
•   Collect data on macromolecular crystals for phase determination, model 
building and refinement.
•   Participate in cooperative research in which the staff scientist's 
expertise is combined with that of members of the NE-CAT consortium 
institutions or general users to improve the processes of protein purification, 
crystallization, and determination of macromolecular structures.
•   Publish results and help prepare presentations and documentation to 
disseminate information about advances to the macromolecular crystallography 
community.

Related Duties:
•   Provide support of sample automounter development.
•   Provide advice and consultation to users and technical support staff.
•   Assist in preparation of research grant proposals and annual reports.
•   Attend and participate in seminars and scientific meetings.
•   Recommend equipment and supplies necessary to further research 
associated with the mission of the facility.
•   Help supervise technicians who will develop user safety procedures, 
calibration procedures, data collection procedures, and both on-line and 
standard documentation.
•   Any other beamline/facility related duties assigned by the supervisors.

Qualifications:
•   Doctorate in Chemistry, Biochemistry, Physics, Biophysics, or a related 
field.
•   At least three years doctoral or post-doctoral experience involving 
macromolecular crystallography.
•   An extensive record of publications of research in the scientific 
literature.
•   Experience with synchrotron X-ray data collection and experience with 
operating synchrotron beamlines is a plus.

For more information about NE-CAT, please see our website:  
https://necat.chem.cornell.edu

This is a 12-month benefits eligible full-time (100%FTE) appointment term which 
is renewable depending on funding and performance.

Salary:  commensurate with experience

Start:  August 1,2019

Interested candidates should submit a cover letter, curriculum vitae, copies of 
relevant publications, and contact information for three references 
electronically to Academic Jobs Online at 
https://academicjobsonline.org/ajo/jobs/14009. Applications will be reviewed as 
they are received and will be accepted until the position is filled.  Please 
direct questions to Frank Murphy, NE-CAT Associate Director 
(fmur...@anl.gov).

Cornell is an equal opportunity, affirmative action educator and employer.







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Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Pavel Afonine]

Hard to see from a static image, but could it be an alternative
conformation?
Pavel

On Tue, Jul 9, 2019 at 2:32 AM Lumbini Yadav  wrote:

> Dear all,
>
>
>
> We have found a huge Fo-Fc density close to cysteine residue (see attached
> image) in the structure with resolution of 1.2A. In the crystallization
> condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and
> protein was in Tris and NaCl. Before freezing the crystals were soaked in
> mother liquor containing sodium dithionite.
>
>
>
> I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
> CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in
> all the screenings we do see some part of Fo-Fc density unaddressed at 3
> sigma.
>
>
>
> Does anyone have an idea about what this density could be? Covalent
> modification?
>
>
>
> Thanks.
>
>
>
> Kind regards,
>
> Lumbini
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Jonathan Cooper]

Refining B-aniso's will clean up a difference map at that resolution.

Sent from Yahoo Mail on Android 
 
  On Tue, 9 Jul 2019 at 16:57, Bonsor, Daniel wrote: 
  #yiv3128113039 #yiv3128113039 -- _filtered #yiv3128113039 {panose-1:2 4 5 3 5 
4 6 3 2 4;} _filtered #yiv3128113039 {font-family:Calibri;panose-1:2 15 5 2 2 2 
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{}#yiv3128113039 
Have you mass-speced the protein before crystallization to make sure it wasn’t 
derivatized during expression and/or purification, or compared the mass spec of 
the crystals verses purified protein? Any fancy reagents or other reductants 
used during purification?
 

 
What about S-Acetyl-cysteine (3-letter code: SCY).
 
  
 
Best,
 
  
 
Dan
 
  
 
Daniel A Bonsor PhD.
 
Sundberg Lab
 
Institute of Human Virology
 
University of Maryland, Baltimore
 
725 W Lombard Street N370
 
Baltimore
 
Maryland
 
MD 21201
 
Tel: (410) 706-7457
 
  
 
  
 
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On Behalf Of Lumbini 
Yadav
Sent: Tuesday, July 09, 2019 5:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fo-Fc density close to cysteine residue
 
  
 
Dear all,
 
 
 
We have found a huge Fo-Fc density close to cysteine residue (see attached 
image) in the structure with resolution of 1.2A. In the crystallization 
condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and 
protein was in Tris and NaCl. Before freezing the crystals were soaked in 
mother liquor containing sodium dithionite.
 
 
 
I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD, 
CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in all the 
screenings we do see some part of Fo-Fc density unaddressed at 3 sigma.
 
 
 
Does anyone have an idea about what this density could be? Covalent 
modification?
 
 
 
Thanks.
 
 
 



 
Kind regards,
 
Lumbini
 
  
 
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[ccp4bb] Cryo-EM director position at the Hauptman-Woodward Medical Research Institute in Buffalo, NY.

[Edward Snell]

Dear CCP4 readers,

The Hauptman-Woodward Medical Research Institute has two current openings, one 
as a synchrotron macromolecular crystallographer at the IMCA beamline in 
Chicago, and announced today, for a cryo-EM center director based in Buffalo 
NY. Both will have the opportunity to interact with our crystallization 
screening center (www.getacrystal.org). Details of 
both positions are available at 
www.hwi.buffalo.edu/careers. The cryo-EM 
center director position is described below. If you know of anyone who may be 
interested in this opportunity or that at IMCA in Chicago, please distribute 
this notice. Applicants should follow the specific directions for each position 
to apply.

The Hauptman-Woodward Medical Research Institute is establishing a regional 
cryo-EM center and is seeking a center director.

The HWI center director will be responsible for operational, scientific, and 
strategic oversight, including growth of the facility, and implementing a 
robust and reliable cryo-EM imaging pipeline. The pipeline is part of the 
Center for Therapeutic Interactions being created at the Institute aimed at 
both the study of interactions and creating them with local, regional and 
international institutions and biotech industry. We expect a broad spectrum of 
projects with a wide range of expertise levels.  The center director reports 
directly to the HWI CEO.

Location: Buffalo, New York.

Responsibilities:


* Supervise the creation of a state-of-the-art cryo-EM 
facility within the Institute and create an efficient research and service 
facility.

* Develop platform that enables inexperienced users to 
address key scientific questions.

* Establish a sample preparation pipeline for experienced 
and inexperienced users alike.

* Collaborate with the Business Development Director to 
attract and retain profitable academic and commercial users for the center.

* Collaborate with complementary resources including a 
high-throughput crystallization center, synchrotron facilities, and a regional 
center for computational resources.

* Ensure instrumentation is operational and produces data 
of the highest possible quality.

* Lead the planning for expansion of the facility to 
include additional microscopes.

* Attract and retain research staff to help operate the 
facility.

* Liaise with financial and accounting staff to implement 
an effective charging scheme for microscope time.

* Advocate for and collaborate on cryo-EM applications 
within the research community.

* Participate in external funding applications, e.g. 
instrumentation grants, large-scale center grants, collaborative grant 
applications, and others.

* Create and implement training programs that promote the 
scientific and commercial program of research capable on the cryo-EM instrument.

* Communicate with vendors and engineers for maintenance 
and upgrade of equipment.

Proven expertise in cryo-EM operation and use is required. Organizational 
skills, and strong written and oral communication abilities, are essential. 
Applicants will be encouraged to develop their own research program and 
collaborate closely with Institute scientists.  Candidates are expected to have 
a PhD in a relevant field and a strong record of scientific productivity.

Benefits:

The Institute has a generous benefits package including fully covered health 
insurance, life insurance and parking. In addition we offer affordable vision 
and dental plans as well as Flexible spending and dependent care accounts. The 
Institute offers a retirement plan.

About HWI and Buffalo, NY:

HWI has celebrated more than 60 years as an independent research institute and 
is continually growing. Located in Buffalo, New York, HWI is at the heart of 
the growing Buffalo Niagara Medical Campus and partners with the University at 
Buffalo, Roswell Park Comprehensive Cancer Center, University of Rochester and 
numerous others. It also has links to industry and operates the IMCA-CAT 
beamline at the Advanced Photon Source outside of Chicago.

Buffalo offers a vast array of community organizations which add to the 
richness of the area and also offer people many opportunities to grow and 
contribute.  Housing is one of the most affordable in the United States.

To apply:

Please send an introductory e-mail, CV and names of 3 references to Jill 
Szczesek, HWI Chief Operating Officer at jszcze...@hwi.buffalo.edu.

To learn more: www.hwi.buffalo.edu/careers


Edward Snell Ph.D.

Biological Small Angle Scattering Theory and Practice, Eaton E. Lattman, Thomas 
D. Grant, and Edward H. Snell.
Available through all good bookshops, or 

[ccp4bb] Engineering Recombinant Proteins: Bioch Soc Training day, London, Nov 4-5

[Amir Khan]

Hi,

This is a reminder and additional details of an upcoming ‘Training Day’ 
organized by the
Biochemical Society.  

Engineering recombinant proteins for structural and functional studies
Tentative venue:  CIWEM, Saffron Hill, Holborn, London  EC1N 8QS (near 
Farringdon station)
Currently, fees are Member £120 / Non member £175 / Student £60, although we 
are working
to reduce the costs.

The programme will address the limiting step in structural studies - the 
production of 
pure and homogenous proteins.  Talks and discussions at this event will explore 
strategies 
to optimize membrane and soluble proteins for crystallization, cryo-EM and NMR 
studies.  
Discussions will include construct optimization, novel thermostability assays, 
crystallization tools and ‘tricks of the trade’ to enable structure 
determination. 

The list of invited speakers are experienced in the structure determination of 
membrane proteins, cytosolic/secreted proteins, and macromolecular signaling 
complexes: 

Edmund Kunji, Cambridge
Daniel Panne, Leicester
Maria Sasi Conte, King’s College
Naomi Chayen, Imperal College
Laura Itzhaki, Cambridge
Chris Tate, Cambridge

More details about the programme and venue will be provided in the coming weeks.

Best wishes,

Amir Khan, Harvard Medical School
Rivka Isaacson, King’s College London


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Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Bonsor, Daniel]

Have you mass-speced the protein before crystallization to make sure it wasn’t 
derivatized during expression and/or purification, or compared the mass spec of 
the crystals verses purified protein? Any fancy reagents or other reductants 
used during purification?
What about S-Acetyl-cysteine (3-letter code: SCY).

Best,

Dan

Daniel A Bonsor PhD.
Sundberg Lab
Institute of Human Virology
University of Maryland, Baltimore
725 W Lombard Street N370
Baltimore
Maryland
MD 21201
Tel: (410) 706-7457


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Lumbini 
Yadav
Sent: Tuesday, July 09, 2019 5:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fo-Fc density close to cysteine residue

Dear all,

We have found a huge Fo-Fc density close to cysteine residue (see attached 
image) in the structure with resolution of 1.2A. In the crystallization 
condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and 
protein was in Tris and NaCl. Before freezing the crystals were soaked in 
mother liquor containing sodium dithionite.

I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD, 
CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in all the 
screenings we do see some part of Fo-Fc density unaddressed at 3 sigma.

Does anyone have an idea about what this density could be? Covalent 
modification?

Thanks.



Kind regards,
Lumbini



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Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Anthony Addlagatta]

Lumbini, 

It would useful to know the distance between the sulfur and center of the Fo-Fc 
map that you have shown. Since you have very high resolution data, the extra 
density could be for a hydrogen atom in CSO-H (sufeneic acid) or anisotropy of 
the oxygen atom. 

Anthony 

From: 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk 
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Tuesday, July 9, 2019 4:48:32 PM 
Subject: Re: [ccp4bb] Fo-Fc density close to cysteine residue 

Any anomalous diffraction? 

On Tue, 9 Jul 2019 at 10:32, Lumbini Yadav < [ mailto:lumbin...@gmail.com | 
lumbin...@gmail.com ] > wrote: 





Dear all, 



We have found a huge Fo-Fc density close to cysteine residue (see attached 
image) in the structure with resolution of 1.2A. In the crystallization 
condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and 
protein was in Tris and NaCl. Before freezing the crystals were soaked in 
mother liquor containing sodium dithionite. 



I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD, 
CXM, SCH, CSU) from the library and also SO 3 , SO 2 and peroxide. But in all 
the screenings we do see some part of Fo-Fc density unaddressed at 3 sigma. 



Does anyone have an idea about what this density could be? Covalent 
modification? 



Thanks. 




Kind regards, 

Lumbini 




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Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Eleanor Dodson]

Any anomalous diffraction?

On Tue, 9 Jul 2019 at 10:32, Lumbini Yadav  wrote:

> Dear all,
>
>
>
> We have found a huge Fo-Fc density close to cysteine residue (see attached
> image) in the structure with resolution of 1.2A. In the crystallization
> condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and
> protein was in Tris and NaCl. Before freezing the crystals were soaked in
> mother liquor containing sodium dithionite.
>
>
>
> I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
> CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in
> all the screenings we do see some part of Fo-Fc density unaddressed at 3
> sigma.
>
>
>
> Does anyone have an idea about what this density could be? Covalent
> modification?
>
>
>
> Thanks.
>
>
>
> Kind regards,
>
> Lumbini
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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[ccp4bb] Fo-Fc density close to cysteine residue

[Lumbini Yadav]

Dear all,



We have found a huge Fo-Fc density close to cysteine residue (see attached
image) in the structure with resolution of 1.2A. In the crystallization
condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and
protein was in Tris and NaCl. Before freezing the crystals were soaked in
mother liquor containing sodium dithionite.



I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in all
the screenings we do see some part of Fo-Fc density unaddressed at 3 sigma.



Does anyone have an idea about what this density could be? Covalent
modification?



Thanks.



Kind regards,

Lumbini



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