[ccp4bb] Doctoral researcher positions - Oulu, Finland
Dear colleagues, There are three (3) doctoral researcher positions available in our teams to study human mono-ADP-ribosyltransferases. The projects focus on biochemical, biophysical and structural studies of the multidomain enzymes and their activation. Selected candidates will also contribute to the development of specific inhibitors for these PARPs. Please feel free to forward this link in case you know someone who may be interested. https://oulunyliopisto.varbi.com/en/what:job/jobID:661910/type:job/where:4/apply:1 Best wishes, Lari Lehtiö & Albert Galera Prat ______ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland https://www.oulu.fi/en/research-groups/lari-lehtio-structural-and-chemical-biology-adp-ribosylation https://twitter.com/LabLehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Dry shipper in limbo
Dear all, Just a note as we have been experimenting with this lately after some lost shipments. We went with Lightbug pro and are ordering more of those. https://lightbug.io/product/pro/ One can customize it to send updates only when moving out of the premises or geofence to significantly lower the costs of updates and there is an API one can use for integration. It is also not limited to Apple ecosystem as we do not need to have an iDevice to connect to it and there does not need to be an iPhone in the storage facility where the lost dewar is. We aim to add a dewar management and tracking system to the IceBear we use to track crystallization, crystals and data (this feature not yet available) and that is also why these features are rather important for us. https://icebear.fi/ This is just one possibility but based on the testing we have been happy with this solution. And of course, since we started using it, the couriers have not lost any dry shippers. Best wishes, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland https://www.oulu.fi/en/research-groups/lari-lehtio-structural-and-chemical-biology-adp-ribosylation https://twitter.com/LabLehtio _ From: CCP4 bulletin board on behalf of Jurgen Bosch Sent: Friday, July 28, 2023 3:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dry shipper in limbo The AirTag is a good idea, I shall implement that. I’ve had samples stuck from Canada to US, also in Memphis. It was just protein on dry ice but needless to say when it arrived it was very dry but no ice. Hopefully you will be lucky and retrieve your samples within the next 14 days. Jürgen __ Jürgen Bosch, PhD, MBA Center for Global Health & Diseases Case Western Reserve University https://www.linkedin.com/in/jubosch/ CEO & Co-Founder at InterRayBio, LLC On Jul 28, 2023, at 07:50, Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote: Hello, I don't do anything MAC but maybe shipping dewars would be a good situation for an Apple Airtag, which I read about recently, or equivalent, if there are any? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com> Sent from Proton Mail mobile Original Message On 28 Jul 2023, 08:56, Savvas Savvides < 9d24f7f13e09-dmarc-requ...@jiscmail.ac.uk<mailto:9d24f7f13e09-dmarc-requ...@jiscmail.ac.uk>> wrote: Dear Kevin, A similar incident from just two weeks ago, in Europe in our case, was resolved by travelling to the regional FedEx package collection/distribution center to recover the dry-shipper in person. This involved gaining access to the FedEx center and talking to the right people. I would absolutely not wait this out because your shipment is probably somewhere in the corner of a distribution center used as a seat by employees taking a break. I can attest to the fact that they do have such corners where “problematic" shipments are piled up! Despite what you were told on the phone or could deduce from any online tracking systems (in our case the dry-shipper was not even trackable), there is still a (very good) chance that your shipment might still be at a regional collection/distribution center. The key is to get to any information about where this place might be, talk to the local people, and find out what the actual route of the shipment might have been after getting picked up from your lab. The routes often involve intermediate collection/distribution sites. To their credit, and in contrast to the general FedEx customer service, the people at the regional FedEx distribution center (including the shift manager) were very empathic and helpful, and used means that go above and beyond SOPs to help. This included sharing photos of the shipment via WhatsApp with drivers/employees of the three previous shifts etc… Despite the volumes of work they handle, drivers and other courier employees actually do remember unusually looking shipments, such as a shipping-case containing a dry-shipper! Best of luck and wishes, Savvas On 28 Jul 2023, at 08:15, Savvas Savvides wrote: Best wishes, Savvas Begin forwarded message: From: "Dr. Kevin M Jude" mailto:kj...@stanford.edu>> Date: 28 July 2023 at 05:16:39 CEST To: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk> Subject: [ccp4bb] Dry shipper in limbo Reply-To: "Dr. Kevin M Jude" mailto:kj...@stanford.edu>> My first adventure in international crystallography is off to an inauspicious start. On Monday, I sent a dry shipper “overnight” from California to Saskatchewan, but it has been stuck in the Mem
Re: [ccp4bb] Crystallography course in Oulu, Finland May29-June2
Dear Colleagues, Just a small update that there is possibility to follow some of the content online. Quick registration is required and please note that the times in the program are in EEST. https://www.oulu.fi/en/events/instruct-eric-course-macromolecular-x-ray-electron-and-neutron-crystallography-2023 Best wishes, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland https://www.oulu.fi/en/research-groups/lari-lehtio-structural-and-chemical-biology-adp-ribosylation https://twitter.com/LabLehtio _ From: Lari Lehtiö Sent: Friday, March 31, 2023 12:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Crystallography course in Oulu, Finland May29-June2 Dear colleagues, We are organizing an Instruct-ERIC course in Oulu on X-ray, neutron and electron crystallography. Please see the details in the web pages. https://instruct-eric.org/events/instruct-eric-course-on-macromolecular-x-ray-electron-and-neutron-crystallography-2023/ https://www.oulu.fi/en/events/instruct-eric-course-macromolecular-x-ray-electron-and-neutron-crystallography-2023 The deadline for applying to the practical on-site part is 10.4.2023. Best wishes, Lari To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Crystallography course in Oulu, Finland May29-June2
Dear colleagues, We are organizing an Instruct-ERIC course in Oulu on X-ray, neutron and electron crystallography. Please see the details in the web pages. https://instruct-eric.org/events/instruct-eric-course-on-macromolecular-x-ray-electron-and-neutron-crystallography-2023/ https://www.oulu.fi/en/events/instruct-eric-course-macromolecular-x-ray-electron-and-neutron-crystallography-2023 The deadline for applying to the practical on-site part is 10.4.2023. Best wishes, Lari To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoctoral researcher position in Oulu, Finland
Dear colleagues, There is a postdoctoral researcher position available in my team. The projects are on structural biology and biophysical studies with some drug discovery aspects. Please forward this link in case you know someone who may be interested. https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=en=14114=1 Best wishes, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland https://www.oulu.fi/en/research-groups/structural-and-chemical-biology-adp-ribosylation https://twitter.com/LabLehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Two doctoral researcher positions - Oulu, Finland
Dear colleagues, There are two doctoral researcher positions available in my team on drug discovery in the field of ADP-ribosylation. The projects are on biophysical studies on enzyme activation as well as in developing specific inhibitors. Please forward this link in case you know someone who may be interested. https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=en=13586=1 Best wishes, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland https://www.oulu.fi/en/research-groups/structural-and-chemical-biology-adp-ribosylation https://twitter.com/LabLehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PhD student position - drug discovery & ADP-ribosylation
Dear colleagues, There is a doctoral researcher position available in my team on drug discovery in the field of ADP-ribosylation. We use extensively crystallography to support inhibitor development efforts. Please forward this in case you know someone who may be interested. https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=en=13109=1 Best wishes, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland https://www.oulu.fi/en/research-groups/structural-and-chemical-biology-adp-ribosylation https://twitter.com/LabLehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Course on X-ray, electron and neutron crystallography - summer 2021
Dear Colleagues, We are organizing an Instruct-ERIC training course on X-ray, electron and neutron crystallography. The course is virtual, but it includes practicals and a possibility to collect data remotely at Diamond Light Source. Participants are selected based on applications while the lectures will be available for a wider audience. As the course is already at the end of June please forward this to the young researchers who could benefit from this opportunity. The deadline for the applications is 30th of May. https://instruct-eric.eu/events/instruct-eric-course-on-macromolecular-x-ray-electron-and-neutron-crystallography Best regards, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland https://www.oulu.fi/university/focusarea/lifelong-health/spearhead-projects/lehtio https://twitter.com/LabLehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Open PhD student position
Dear all, There is an open PhD student position in our team within a project focusing on structure and function of human tankyrases as well as on inhibitor discovery. https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=en=10302=1 Please feel free to forward this link to potentially interested young scientists. Best regards, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland https://www.oulu.fi/university/focusarea/lifelong-health/spearhead-projects/lehtio https://twitter.com/LabLehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PhD student position in Finland
Dear colleagues, We have a 4-year PhD student position for 2020-2023 open in my team. The project focuses on structural and functional characterization of human ADP-ribosyltransferases. For more details and application form please see the web application portal: https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=7633=en Note that applications received by email will not be considered. Best regards, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://www.oulu.fi/biocenter/groups/lehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Crystallography course in Oulu, Finland
Dear all, This is a reminder of the international crystallography course in Oulu, Finland. The program has been updated and we have extended the deadline to 3.3.2019. Please see the web pages for details: https://www.oulu.fi/biocenter/protein-crystallography/events/x-ray-neutron-2019 Best regards, Lari __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://www.oulu.fi/biocenter/groups/lehtio _ From: Lari Lehtiö Sent: Thursday, January 31, 2019 9:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Crystallography course in Oulu, Finland Dear all, We are pleased to announce a course: “X-ray and neutron crystallography: from data collection to structures”. This intensive course is organized from May-13 to May-17, 2019 at the Faculty of Biochemistry and Molecular Medicine, University of Oulu in Oulu, Finland. It is organized in the context of the iNEXT Horizon2020 project (http://www.inext-eu.org), together with Diamond Light Source, The European Spallation Source, Biocenter Oulu and the Health and Biosciences Doctoral Programme of the University of Oulu. The course will include an introduction on the methods of protein and neutron crystallography and best practises in data collection are discussed. Tutorials include data processing, experimental phasing, molecular replacement phasing and neutron structure refinement. Remote data collection (Diamond Light Source) of crystals from participating students is scheduled for Thursday. The course provides extensive opportunities for the students to work with the presented software in our Linux class room and to interact with the expert teachers. Students are encouraged to send crystals in advance, which will then be shipped to Diamond Light Source, for remote X-ray data collection. Students are also encouraged to bring their own raw X-ray data images which are difficult to process or their own X-ray data sets for which molecular replacement calculations have turned out to be difficult. There is no registration fee. Applications for the course can be sent before 24.02.2019. The course is aimed at PhD students and postdocs working on structural biology projects using X-ray or neutron diffraction methods. The application should include a CV, a motivation letter and a letter from the supervisor. Please also indicate if you plan to send crystals. Detailed information on how to apply, including a list of confirmed lectures and tutorials, is available at: https://www.oulu.fi/biocenter/protein-crystallography/events/x-ray-neutron-2019 On behalf of the organizers, Lari Lehtiö __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://www.oulu.fi/biocenter/groups/lehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Crystallography course in Oulu, Finland
Dear all, We are pleased to announce a course: “X-ray and neutron crystallography: from data collection to structures”. This intensive course is organized from May-13 to May-17, 2019 at the Faculty of Biochemistry and Molecular Medicine, University of Oulu in Oulu, Finland. It is organized in the context of the iNEXT Horizon2020 project (http://www.inext-eu.org), together with Diamond Light Source, The European Spallation Source, Biocenter Oulu and the Health and Biosciences Doctoral Programme of the University of Oulu. The course will include an introduction on the methods of protein and neutron crystallography and best practises in data collection are discussed. Tutorials include data processing, experimental phasing, molecular replacement phasing and neutron structure refinement. Remote data collection (Diamond Light Source) of crystals from participating students is scheduled for Thursday. The course provides extensive opportunities for the students to work with the presented software in our Linux class room and to interact with the expert teachers. Students are encouraged to send crystals in advance, which will then be shipped to Diamond Light Source, for remote X-ray data collection. Students are also encouraged to bring their own raw X-ray data images which are difficult to process or their own X-ray data sets for which molecular replacement calculations have turned out to be difficult. There is no registration fee. Applications for the course can be sent before 24.02.2019. The course is aimed at PhD students and postdocs working on structural biology projects using X-ray or neutron diffraction methods. The application should include a CV, a motivation letter and a letter from the supervisor. Please also indicate if you plan to send crystals. Detailed information on how to apply, including a list of confirmed lectures and tutorials, is available at: https://www.oulu.fi/biocenter/protein-crystallography/events/x-ray-neutron-2019 On behalf of the organizers, Lari Lehtiö __ Lari Lehtiö, Professor Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://www.oulu.fi/biocenter/groups/lehtio _ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoctoral position in Oulu, Finland
Dear all, We have a position open for a postdoctoral researcher in a team focusing on structural biology and drug discovery. Information on our team and projects can be found from our web pages: http://www.oulu.fi/biocenter/groups/lehtio More details regarding the position can be found in the following link. Application forms are available also through the link and applications are accepted only through the web-based system. https://www.saimanet.com/certiahome/open_job_view.html?id=5405 Best regards, Lari __ Lari Lehtiö, PhD, Docent/Adjunct Professor Biocenter Oulu Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://www.oulu.fi/biocenter/groups/lehtio _
[ccp4bb] PhD student position in Oulu, Finland
Dear all, We have a position open for a PhD student in the field of structural biology and drug discovery. The project focuses on structure and inhibition of ADP-ribosyltransferases. Information on our team and projects can be found from our web pages: http://www.oulu.fi/biocenter/groups/lehtio More details regarding the position can be found in the following link. Application forms are available also through the link and applications are accepted only through the web-based system. https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5396 Best regards, Lari __ Lari Lehtiö, PhD, Docent/Adjunct Professor Biocenter Oulu Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://www.oulu.fi/biocenter/groups/lehtio _
[ccp4bb] Postdoctoral and PhD student positions - Oulu, Finland
Dear all, We have positions open in my group for a PhD student and for a postdoctoral researcher. The project focuses on structure and inhibition of ADP-ribosyltransferases.? Information on our team and projects can be found from our web pages: http://www.oulu.fi/biocenter/groups/lehtio More details regarding the open positions can be found in the following links. Application forms are available also through the links and applications are accepted only through the web-based system. Postdoctoral position: https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=4031=en PhD student position: https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=4032=en Best regards, Lari __ Lari Lehtiö, PhD, Docent/Adjunct Professor Biocenter Oulu Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://www.oulu.fi/biocenter/groups/lehtio _
[ccp4bb] NEXT course: “X-ray and neutron diffraction studies of macromolecules: from data collection to structures”
Dear All, A reminder of the upcoming course we are organizing in Oulu. Please notice that we have extended the deadline for application to 19.2.2017. This intensive course is organized from May-15 to May-19, 2017 at the Faculty of Biochemistry and Molecular Medicine, University of Oulu in Oulu, Finland. It is organized in the context of the iNEXT Horizon2020 project (http://www.inext-eu.org ), together with Diamond (Oxford, UK) and Biocenter Oulu. The course will include an introduction on the methods of protein crystallography (Rupp), neutron crystallography (Oksanen/Podjarny) and SAXS/SANS-approaches (Svergun). Also data collection at synchrotrons (Thunnissen), new perspectives when using the new long-wavelength beamline at Diamond (Wagner) and when using XFEL-technology (Hajdu) will be addressed. Tutorials include the validation tools of the PDB-deposition server (Rupp), as well as data processing (DIALS, Waterman; XDS, Rower), experimental phasing (SHELX, Gruene), molecular replacement phasing (CCP4, Lebedev) and neutron structure refinement (Oksanen, Podjarny). Remote data collection (Diamond, Aller, Powell) of crystals from participating students is scheduled for the last day of the course. The course provides extensive opportunities for the students to work with the presented software in our linux class room and to interact with the expert teachers. Students are encouraged to send crystals in advance, which will then be shipped to Diamond, for remote X-ray data collection. Students are also encouraged to bring their own raw X-ray data images which are difficult to process or their own X-ray data sets for which molecular replacement calculations have turned out to be difficult. There is no registration fee and we aim to cover also the accommodation costs and meals of the students. Application for the course can be sent in January and the deadline is 19.02.2017. The course is aimed at PhD-students and postdocs working on structural biology projects using X-ray or neutron diffraction methods. The application should include a motivation letter and a letter from the supervisor. Detailed information on how to apply, including a list of confirmed lectures and tutorials, is available at http://www.oulu.fi/biocenter/instruct-nac/courses/oulu . On behalf of the local organisers, Rik Wierenga and Lari Lehtiö? __ Lari Lehtiö, PhD, Docent/Adjunct Professor Biocenter Oulu Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://cc.oulu.fi/~llehtio/ _
[ccp4bb] Postdoc and PhD student positions
Open positions in the laboratory of Lari Lehtiö at the Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu,University of Oulu, Finland. The research group focuses on structure, function and inhibition of ADP-ribosyltransferases (ARTDs/PARPs). We use protein X-ray crystallography, activity assays and complementing biophysical techniques to understand how the signaling enzymes work. We also use screening of compound libraries and structure-based design of specific inhibitors for the enzymes to be used as chemical probes as well as drug leads. More information of our research is available on the web pages (http://www.oulu.fi/biocenter/groups/lehtio). Postdoctoral researchers We have 2 positions for postdoctoral researchers. One position is available immediately until 31.12.2016 with possible extension depending on funding. Second positions is for 1.9.2015 until 31.8.2018 with possible extension depending on funding. We are looking for researchers holding a doctoral degree or soon to receive one and having interest in structural biology and drug discovery. Work includes cloning, expression, purification and characterization of recombinant proteins as well as structural studies using X-ray crystallography and small-angle X-ray scattering. Experience in protein characterization, medicinal chemistry or structural biology is considered beneficial. The salary will be based on the demand level 5 of the salary system in Finnish Universities and includes a component based on personal performance. The application should include 2 pdf files 1) a motivation letter (1 page) describing prior knowledge and interests 2) a complete CV containing contact information of two references. Application should be sent to Lari Lehtiö by email (lari.lehtio(at)oulu.fi) with a subject line “Application for a Postdoctoral position”. First position is filled as soon as a suitable candidate is found. For the second position the applications are accepted until 14.6.2015. PhD student A position is available for a PhD student with funding currently available for three years. Position is available immediately and it will contain a trial period. We are looking for a student holding a MSc degree and with interest in structural biology and drug discovery. Work includes cloning, expression, purification and characterization of recombinant proteins as well as structural studies using X-ray crystallography. The aim of the project is to develop selective inhibitors for human mono ADP-ribosyltransferases. The salary will be based on the demand levels 2-4 of the salary system in Finnish Universities and includes a component based on personal performance. The application should include 2 pdf files 1) a motivation letter (1 page) describing prior knowledge and interests 2) a complete CV containing contact information of two references. Application should be sent to Lari Lehtiö by email (lari.lehtio(at)oulu.fi) with a subject line “Application for a PhD position”. Applications are accepted until 14.6.2015. Best regards, Lari __ Lari Lehtiö, PhD, Docent/Adjunct Professor Biocenter Oulu Faculty of Biochemistry and Molecular Medicine P.O.Box 5400 FIN-90014 University of Oulu Finland http://cc.oulu.fi/~llehtio/ _
Re: [ccp4bb] side chain density
Hi, There has been quite a lot of discussion about this and I think different opinions exist. I would try to keep the side chains, if there is some evidence where they are. Otherwise I would just delete atoms and I would not mutate them to alanine. http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20437.html Best regards, Lari __ Lari Lehtiö, PhD, Adjunct Professor Biocenter Oulu Department of Biochemistry P.O.Box 3000 FIN-90014 University of Oulu Finland http://cc.oulu.fi/~llehtio/ _ Quoting Faisal Tarique faisaltari...@gmail.com: Dear all i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22 and 25 respectively..the Ramachandran plot shows 90% of the residues in the most favorable region and with 6 residues in generously allowed and no residues in disallowed region. But in some areas i can see density missing for side chains ( in loop regions )..i have question do i need to mutate them to alanine or leave them as such..The density fit analysis in COOT ( traffic light) showing those regions with side chain as red.. thanx in advance Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] linux flavors
Hi, Slightly deviating from the original thread perhaps: I am having trouble with recent releases of Ubuntu on my Toshiba Satellite laptop, mainly associated with ACPI. The internet is awash with discussions on how to fix the problems with ACPI (fan speed, screen brightness etc). None of the solutions that have been suggested, work for me. I still run Ubuntu 8.04, which is ok, but all versions after that effectively mean the screen brightness is stuck at one level and the fan either runs on full speed or not at all. Other people in the lab have reported similar problems with their laptop (various makes). Does anyone know of a linux distribution where everything just works, without having to go back to the dark ages of linux where multimedia etc are not supported? Thanks, Johan Gentoo? http://www.gentoo.org/main/en/about.xml ~L~ __ Lari Lehtiö Pharmaceutical Sciences, Department of Biosciences Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 http://www.users.abo.fi/llehtio/ __
Re: [ccp4bb] Unexplained density
Hi, Anomalous map might give you some idea if it can be zinc. ~L~ __ Lari Lehtiö Pharmaceutical Sciences, Department of Biosciences Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 http://www.users.abo.fi/llehtio/ __ Quoting Dr. STEPHEN SIN-YIN, CHUI chui...@hkucc.hku.hk: Dear Daniel Is the omit map for the model with and without the zinc ions possible to confirm its existence? I am curious. What is the resolution of dataset? stephen Quoting Daniel Bonsor bon...@bbri.org: Hello again I currently have some unexplained density in my structure. As you can hopefully see from the images (see file), the density is dumbbell shaped. Whatever it is, it is coordinated by Asp and Glu residues. To me it looks like each lobe is a ring structure. The crystallization condition was: 6.5% PEG 8K, 10mM ZnSO4, 100mM sodium cacodylate pH 6.5, 100mM Am2SO4, 1% glycerol, with 20% glycerol as cryo. Protein was originally in 50mM Tris, 50mM NaCl pH 7.5. I originally placed a single Zn at the center of each lobe. Though after refmac, the Zn was displaced to one side. Two zincs in each dumbbell may have worked, but I am dubious about two zinc atoms being 4A apart and there is still some unexplained density. Are there any possible cyclization reactions of Tris, cacodylate or glycerol may have undergone to explain the density? Or is it simply a highly ordered water network? Or is there some other explanation? Thanks in advance Dan -- Dr. Stephen Sin-Yin Chui Research Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
Re: [ccp4bb] Buried surface area (BSA) vs. oligomeric interface
Hi, just a place I would perhaps start looking: http://www.ebi.ac.uk/msd-srv/prot_int/picite.html ~L~ __ Lari Lehtiö Pharmaceutical Sciences, Department of Biosciences Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 http://www.users.abo.fi/llehtio/ __ Quoting Sollepura Yogesha yoge...@scripps.edu: Dear All, We found that our structure is having a large buried surface in its dimer interface (~18% as calculated by AREAIMOL). This dimer has not been observed in earlier studies and right now we have less data to support this strong interface formation. I am looking for some literature which provide guidelines to understand the relation of BSA or crystal contacts with oligomeric interfaces. Any suggestion is highly appreciated Thanks in advance Yogi
Re: [ccp4bb] Protein crystallizes while concentration
Dear Rajkumar, I would use dialysis buttons. E.g. http://hamptonresearch.com/product_detail.aspx?cid=10sid=63pid=111 Put your protein to the button and seal it with a piece of dialysis membrane. Place this to a linbro plate (easy to look with a microscope), fill the well with low salt buffer and seal with a cover slip. To make the diffusion slower, you can put the dialysis button inside a dialysis tubing with some high salt buffer and place this to a bigger volume of low salt buffer. ~L~ __ Lari Lehtiö Pharmacy, Department of Biochemistry and Pharmacy Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 http://www.users.abo.fi/llehtio/ __ Quoting E rajakumar e_rajaku...@yahoo.com: Dear All I am Rajkumar, working on the protein which has unusual behavior while concentration. When I kept protein in 15 mM Tris 7.5, 150 mM NaCl and 5 mM DTT, the solubility of the protein is decreases drastically and tend to crystallize while concentration. Protein cannot be concentrated more than 3 mg/mL, however I noticed white turbid protein if I force to concentrate 3mg/mL. When I observed this white turbid solution under the microscope, I noticed shower of tiny protein crystals which are needle in shape. I screened freshly purified protein (2.5 mg/mL) in different Hampton and Qiagen screens, strangely none of the conditions gave the crystals. I concentrated left over protein at 15oC at 3 mg/mL and kept in the 4oC for 4 days again I noticed shower of crystals. This protein solubility is increased to ~20mg/mL when I kept in 15 Tris 7.5, 400 mM NaCl, 5% Glycerol and 5 mM DTT, but did not crystallize while concentration and also after screening with Hampton and Qiagen screens. My queries are 1. How do I get the crystals in the crystallization set up rather than while concentration, so that I can control the diffusion and finally nucleation? 2. Could anybody give me suggestions on seeding in this type of situation? 3. Any comments on reverse vapor diffusion for this type of protein are most welcome. So I can keep protein in high ionic strength (~400 mM NaCl)and diffuse against low Ionic strength or deionized water? Or any other protocol? Any suggestions are well appreciated. Thanking you in advance Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) Get your new Email address! Grab the Email name you#39;ve always wanted before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/
Re: [ccp4bb] off topic: multiple structural sequence alignment
I ended up using multiprot and staccato recently http://bioinfo3d.cs.tau.ac.il/MultiProt/ There is a server for multiprot, but I downloaded the applications. I still ended up doing quite a bit manual editing in filling the gaps in the structures etc. I stumbled also over a link about the matter comparing different programs (by Dr Elaine Meng): http://www.cgl.ucsf.edu/home/meng/grpmt/structalign-content.html ~L~ __ Lari Lehtiö Pharmacy, Department of Biochemistry and Pharmacy Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 http://www.users.abo.fi/llehtio/ __ Quoting Ronnie Berntsson r.bernts...@rug.nl: Dear all, A bit off the topic question perhaps. I am trying to find a program which can do multiple structural sequence alignments. What I would like is a program which can take as input PDB codes (or files), and which will output a multiple sequence alignment in FASTA format with the full sequences of the supplied proteins intact. Preferably said server/program should be able to handle at least 20 input pdbs at once. I've been looking around, but have so far failed to find a program which does this. If anyone knows of a program or server which could handle this, I would be very grateful. Cheers, Ronnie Berntsson
Re: [ccp4bb] anisotropic diffraction in refinement
There is a ellipsoidal truncation and scaling server you might want to try. http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/ ~L~ __ Lari Lehtiö Pharmacy, Department of Biochemistry and Pharmacy Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 __ Quoting Justin Hall hallj...@onid.orst.edu: Dear All; I am working with a data set which is anisotropic. The resolution limits are ~ 2.75 by 3.45 A. The I have integrated (using Mosflm) the data out to 2.75 A, the data therefore includes a mix of real (I/sig 1) and imaginary (I/sig ~1) data past the 3.45 A resolution bin. I am concerned that the presence of the poor quality data in the outer shells will cause my good data to 2.75 A resolution to be down weighted in refinement. Since anisotropic resolution limits do not seem to be an option, are there other tools that would allow proper weighting for this situation? Cheers~ ~Justin Hall Oregon State University
Re: [ccp4bb] hydrogen bond between aspartate side chain and main chain carbonyl group?
Hi, Not my structure, but noticed similar bond in glycerol dehydratase, when comparing structures. PMID: 16414072 pdb 1R9E and resid 506. (resolution 2.4 Å) Buried rather hydrophobic environment and Asp make H-bonds to serine hydroxyl and carbonyl. ~L~ __ Lari Lehtiö Pharmacy, Department of Biochemistry and Pharmacy Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 __ Quoting b...@freesurf.fr: Hi Frank, such interactions are certainly possible, in particular if additional H-bonding side chains are available to stabilize the arrangement. I'm not aware of any examples involving main chain carbonyls, but for a discussion of carbonyl-carbonyl side chain interactions see the following paper: Flocco, M.M. and Mowbray, S.L. (1995) Strange Bedfellows: Interactions between Acidic Side-Chains in Proteins, J. Mol. Biol. 254 96-105 Best wishes, Sebastiaan Werten. - Original Message - From: Frank Lee To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, April 25, 2009 7:47 AM Subject: [ccp4bb] hydrogen bond between aspartate side chain and main chain carbonyl group? Hi, In a new structure we observed a hydrogen bond between an aspartate side chain and a main chain carbonyl group. Because both of them are electronegative, I am puzzled. My questions are: does this hydrogen bond make sense at all? any precedent for such a hydrogen bond? I would appreciate your help very much! Frank
