[ccp4bb] 3D printing format
Sorry for the rather random question but has anyone out there used a 3D printer to print a protein structure? If so, what format did you need to convert the PDB into to allow the printer to interpret the data? Many thanks, Joe P Joe Patel FBLG Specialist _ AstraZeneca RD | Innovative Medicines | Discovery Sciences Boston RD, Discovery Sciences 35 Gatehouse Drive, Waltham MA 02451 Tel 1-781-839-4129 joe.pa...@astrazeneca.commailto:steven.kazmir...@astrazeneca.com P Please consider the environment before printing this e-mail Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
Re: [ccp4bb] Unusual electron density - any guesses??
Is that a glycine in the sequence next to the Glu/Gln? Have you tried building a 50% occ of the backbone in that region in two conformations, and then a water molecule further up into the feature. The density over the carbonyl looks weak and you have some negative density there that might indicate mixed conformation. Just an idea, hard to tell from still images if my idea would work. Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jose Artur Brito Sent: Friday, October 25, 2013 1:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unusual electron density - any guesses?? Dear All, I'm refining an X-ray structure to 1.6A resolution in BUSTER-TNT v2.10. The model is pretty much finished but I see a strange electron density that I can't imagine what it is. Please take a look at four snapshots in http://www.itqb.unl.pt/~jbrito/ITQB/ . Any pointers/guesses are most welcome. In short, I see an oblong piece of density coming straight out of the main-chain!! It doesn't refine as a chain of waters and any small piece of PEG doesn't refine properly either (actually, not sure if this would make any sense but since the crystallization condition is PEG3350 and gave it a try!!). The crystallization condition is PEG3350, Bis.Tris buffer, (NH4)2SO4 and NaI. The protein was purified from recombinant expression in E. coli with trivial reagents: Tris and Bis.Tris buffers, NaCl, glycerol, ... Wishing you all an excellent weekend, best regards, Jose -- * José Artur Brito, PhD* * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal* * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbr...@itqb.unl.pt * * URL: http://mx.itqb.unl.pt *
[ccp4bb] Supplier for X-ray sensitive paper
Hi All, I have done a few searches of the archive and googled a few times but not found what I am looking for. Could someone point me in the direction of a supplier of the X-ray sensitive paper I have used in the past to confirm beam position on a home source. I am specifically after this type of paper rather than X-ray film so as not to have to go through any developing stage and quickly visualize the location of the beam at different points beyond the position of the goniometer towards the detector. A USA supplier would be great but any would do. Many thanks, Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
Re: [ccp4bb] Ligand geometry obs. vs. ideal
Hi Yuri, If you have access to mogul you can get an understanding of what your geometry should be based on the small molecule database. Of course not everything is well represented so if your ligand is unusual this will flag up in lower statistical significance. Mogul will allow you to understand how far you are from ideal. Not really sure if this is what you might be after Joe P -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri Pompeu Sent: 12 September 2012 19:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ligand geometry obs. vs. ideal Hi everyone, I am trying to show that a ligand underwent catalysis during a soaking experiment. One of the things I would like to show is the geometry of the ligand, bond angles/lengths, dihedrals, etc... One of my models has a hi-res of 1.18A and the ligand density is really clear and complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot
Re: [ccp4bb] Lithium versus Sodium
Hi Scott I may be completely wrong but I worked on a lithium and sodium inhibited enzyme during my PhD. At the time, it was considered that your chances of actually seeing density for a Li+ ion were slim to nil. Only 2 electrons makes them as tough as hydrogens. My efforts went into trying to prove I had a sodium ion bound over magnesium which is the catalytically active ion Do you have ultra-high resolution? Something I did not Are there many examples in the pdb of proteins with Li+ refined? Sorry no real help to you, but curious since it brings up old memories... Joe P Dr Joe Patel _ AstraZeneca Discovery Sciences, Structure Biophysics UK 50S38, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG Tel +44 (0)1625 233543 Fax +44 (0)1625 230164 joe.pa...@astrazeneca.com mailto:name.surn...@astrazeneca.com P Please consider the environment before printing this e-mail From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Scott Pegan Sent: 12 January 2012 06:10 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Lithium versus Sodium Hey all, Does anyone know of a good article that deals with differentiating between a lithium ion and sodium ion for density in a X-ray structures? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254 -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
[ccp4bb] Permanent Position for NMR spectroscopist at AstraZeneca, Alderley Park, UK
There is currently a position available within the Structure Biophysics group. The application deadline is 30th January 2012. Please use the AstraZeneca Careers website to submit your application, if you are interested. The link to the job, with a role description can be found using the link below. http://gs.globalsuccessor.com/fe/tpl_astrazenecav2.asp?newms=jjid=58285 newlang=1 Thanks, Joe P Dr Joe Patel _ AstraZeneca Discovery Sciences, Structure Biophysics UK 50S38, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG Tel +44 (0)1625 233543 Fax +44 (0)1625 230164 joe.pa...@astrazeneca.com mailto:name.surn...@astrazeneca.com P Please consider the environment before printing this e-mail -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [ccp4bb] strange density
Hi Alex, Was it purified via a Ni2+ resin? Is the protein oligomeric in solution? Could it have stripped an ion out during purification and brought it all the way through to crystallisation? Have you tried refining a Ni2+ in the location? JP -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Alex Singer Sent: 24 February 2011 00:35 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] strange density Hi -- I have a high resolution structure (1.6 A) where I'm ready to deposit except I have some very strange density, shown in the two pictures here -- sort of a sphere with a split cresent around it, falling between molecule A and B His 138 imidazole rings. The sphere is modeled as a Cl atom, more for kicks because resulting 2Fo-Fc maps still have considerable positive difference density throughout the sphere. There are 4 molecules in the AU, the imidazole ring of H138 in molecules C and D point into a solvent channel. Crystallization conditions are 0.2M Mg Chloride, 0.1M Bis-Tris pH6.5, 25% PEG3350, cocrystallized in 2.5mM Glycero-3Phosphocholine and cryoprotected by dipping in Paratone_N oil. Let me know what you're thoughts are and thank you for your help. Alex Singer -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033
Re: [ccp4bb] question about the zinc binding protein
BTWBy the way I think, not a buffer abbreviation -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Enrico Stura Sent: 01 April 2010 11:02 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] question about the zinc binding protein What is 1mM BTW? I am not familiar with this abbreviation. PBS phoshate buffered saline (Phosphate + NaCl) not suitable for zinc binding proteins BBS borate buffered saline (Borate + NaCl) wrong pH for zinc binding. BTW ? (? ? ?) No idea what this is. Charles, do you know if it includes HEPES or Phosphate? Enrico. On Thu, 01 Apr 2010 11:06:10 +0200, Charles Allerston charles.allers...@sgc.ox.ac.uk wrote: Hi, are you sure it is your protein precipitating? You will get a cloudy precipitate appearing in HEPES and Phosphate buffers on addition of ZnCl, without protein. cheers charlie dengzq1987 dengzq1...@gmail.com 3/31/2010 5:08 pm hello everyone, recently i purify a protein conteining zinc binding domain,and i want to determine its structure.i get the crystal,but poor diffraction.so i try to adding zinc into the protein to optimize the crystal,but the protein precipitate immidiately even the znic is 1 mM.BTW,we use the protein to do zinc scan,we don't find the zinc. does anyone have some advice? 2010-03-31 dengzq1987 -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449 Lab LTMB, SIMOPRO, IBiTec-S, CEA Saclay, 91191 Gif-sur-Yvette Cedex FRANCE http://www-dsv.cea.fr/en/ibitecs/82 http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
