[ccp4bb] Co-Crystallization with drug molecule
Hi everyone, I am trying to crystallize a protein with a drug molecule. The protein concentration is 15.5 mg/ml, the drug stock concentration is 10 mM, and the drug is dissolved in DMSO. I am adding the drug to a final concentration of 1 mM in 100 ul of protein, and the DMSO volume is 10 ul for Co-crystallization. I want to know how much DMSO is permissible during co-crystallization with the drug and if DMSO can poison crystal formation. I have not been successful in getting crystals with inhibitors till now, but I obtained crystals of protein without DMSO, and those diffracted to 2.5A. Thanks, *Dr. Amit Gaur,* *Research Scientist* *Center for Biotechnology and **Interdisciplinary Studies,* *Rensselaer Polytechnic Institute,* *1623 15th Street, Troy, NY, 12180* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Hydrophobic/ vander waal forces
Hi everyone, I hope everything is going well with all of you. I want to know that, Are hydrophobic and vander waal forces are similar? and what is criteria for formation of these and interatomic distances needed to form these interactions between amino acids? What kinds of atoms have propensity to form these interactions? Thank you, -- *Dr. Amit Gaur* *Research AssociateThomas Jefferson University* *Department of Translational medicine* *1020, Locust Street, Jefferson Alumni Hall* *Philadelphia, PA 19107* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] hydrophobic forces
Hi All, I have a question that, I have a loop region with hydrophilic residues(TNETRERE) that lie close to methionine. Can, repulsive forces may occur because between methionine and hydrophilic residues? -- *Dr. Amit Gaur* *Post Doctoral Researcher* *Thomas Jefferson University* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Homology modeling
Hi All, I am trying to generate a model using comparative modeling. Can anybody suggest the quality of the model based on procheck summary. +--<<< P R O C H E C K S U M M A R Y >>>--+ || | /var/www/PROCHECK/Jobs/7358861/7358861.pdb 1.5 1253 residues | || *| Ramachandran plot: 87.9% core 10.2% allow1.4% gener0.4% disall | || *| All Ramachandrans: 67 labelled residues (out of1235) | +| Chi1-chi2 plots: 3 labelled residues (out of 771) | | Side-chain params:5 better 0 inside 0 worse | || *| Residue properties: Max.deviation: 4.9 Bad contacts:0 | *| Bond len/angle:9.9Morris et al class: 1 1 2 | || | G-factors Dihedrals: -0.13 Covalent: -0.07Overall: -0.10 | || *| Planar groups:90.0% within limits 10.0% highlighted 13 off graph | || ++ + May be worth investigating further. * Worth investigating further. Thanks, To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] technical question
Thanks every one. I tried this and worked pretty well. On Fri, Nov 29, 2019 at 4:42 PM Robbie Joosten wrote: > Or use the residue name MHO if SME has the wrong hand around the sulfur. > > Cheers, > Robbie > > On 29 Nov 2019 21:47, Paul Emsley wrote: > > On 29/11/2019 18:06, amit gaur wrote: > > > I want to replace a particular methionine in a pdbwith methionine > sulfoxide( an oxidized form of > > methionine). Can body please tell me how to do this? I am familiar with > pymol, chimera and coot software. > > In Coot: > > Extensions -> Modelling -> Replace Residue -> SME -> Mutate > > > > 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: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- *Dr. Amit Gaur* *Post Doctoral ResearcherPI: Dr. Ji-Fang ZhangThomas Jefferson University* *1020, Locust Street, Suite 418* *Philadelphia, PA 19107* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] technical question
Hi everbody, I want to replace a particular methionine in a pdb with methionine sulfoxide( an oxidized form of methionine). Can body please tell me how to do this? I am familiar with pymol, chimera and coot software. -- *Amit Gaur* *Post Doctoral ResearcherThomas Jefferson University* *1020, Locust Street, Suite 418* *Philadelphia, PA 19107* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Dimer in SDS-PAGE
Hi all, I am trying to purify a potassium ion channel from insect cell using baculovirus expression system. I am not seeing monomer of this protein in SDS instead a dimer appears.So,I increased DTT in SDS buffer but no change and dimer was intact. In size exclusion this protein appeared as a tetramer which is common oligomerizaton of potassium channel family with GYG motif. Can any body suggest what should I do in this case? Thanks and regards, -- *Dr. Amit Gaur* *Post Doctoral ResearcherPI: Dr. Ji-Fang ZhangThomas Jefferson University* *1020, Locust Street, Suite 418* *Philadelphia, PA 19107*
