Re: [ccp4bb] Dose anyone see this ligand before?
Remember, that MPD is chiral, so you have two possibilities at C4. After putting MPD into your model the FoFc-density should clearly tell you (your resolution looks better than 2 A), if the group on the left in your picture is a phosphate / sulfate or if it only has a carbon in the middle of the tetrahedrally bound atom. Check for hydrogen bonding partners, which help to identify hydroxy groups. greetings Gottfried At Wednesday, 17-07-2013 on 06:14 sonali dhindwal wrote: hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” - From: sonali dhindwal To: "ccp4...@hotmail.com" Sent: Wednesday, 17 July 2013 9:44 AM Subject: Re: [ccp4bb] Dose anyone see this ligand before? hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” - From: Wei Feng To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 16 July 2013 9:05 PM Subject: [ccp4bb] Dose anyone see this ligand before? Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei
Re: [ccp4bb] practical protocol to remove cell culture derived Threonine from the protein
Dear Wenhua, in extension to the post from Herman, you could try to remove the threonine with a separate enzyme, for instance threonine oxidase or amino acid deaminase. Their reaction products probably also bind less tightly. The question is, how fast the release of threonine from your protein is. greetings Gottfried Am Dienstag, dem 26-06-2012 um 11:08 schrieb Wenhua Zhang: Dear ALL, The threonine is found in the active site of my protein structure from the crystallization in the absence of any threonine containing chemicals. I presume that's why there was no signals detected with the ITC experiment in which I titrate my protein with Threonine. In the in vitro biochemical assay, threonine is one of the substrates in the reconsitituted system. So could anyone offer me a practical protocol to remove the threonine from the protein for further experiment to confirm the binding of Threonine to my protein by ITC. Thank you all. Wenhua Ph. D student in structural biology Paris-Sud XI, France
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
One could consider RIP (phasing using radiation induced damage) as SIR technique. At short wavelengths ( Hey! > > I was just wondering, do you know of any recent (~10y) publication that presented a structure solution solely based on MIR? Without the use of any anomalous signal of some sort? > > When was the last time you saw a structure that was solved without the use of anomalous signal or homology model? Is there a way to look up the answer (e.g. filter settings in the RCSB) I am not aware of? > > Thanks, > S. > > (Disclaimer: I am aware that isomorpous data is a valuable source of information)
