What is the single Latin word for troll? Kendall
On Apr 1, 2012, at 3:06 PM, "Kevin Jin" <kevin...@gmail.com<mailto:kevin...@gmail.com>> wrote: “I hope and believe that this is not the case. Even basically-trained crystallographers should be able to calculate and interpret difference maps of the kind described by Bernhard. And with the EDS and PDB_REDO server, one does not even need to know how to make generate a difference map...” You are right! Actually, I am not an experienced protein crystallographer. I have learnt a lot from CCP4BB. I may have paid too much attention to bonding angle and bond length, like in small molecule. This may be an example to share with you. When I worked on those nitroreductase complexed with FMN in 2009 (?), I always observed that the flavin ring presented a strange geometry after refinement. Indeed, I had used the definition of FMN from CCP4 library all the time. In some cases, the methyl group at position of either 7a or 8a was bent off the aromatic ring, if the whole the rest of flavin was restrained in a flat plane. According to my limited knowledge from organic chemistry, carbon of 7 and 8 on the flavin ring is sp2 hybridized in a coplanar manner. How could those methyl groups be bent as sp3 hybridization? Any chemistry behind? With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron density map was a bent along the N5-N10 axis. The bend angle was around ~16 degree. Again, I questioned myself why it was bent? Should this be correct? According to my limited knowledge in chemistry, N10 should be sp3 configuration even if FMN is in its oxidization form, in which the flavin ring should be bent. A quick “google” immediately gave me a link to a very nice paper published by David W. Rodgers in 2002. http://www.jbc.org/content/277/13/11513.full.pdf+html According to this paper, Yes! “In the oxidized enzyme, the flavin ring system adopts a strongly bent (16°) conformation, and the bend increases (25°) in the reduced form of the enzyme,…” When I reported this in the group meeting, I was laughed and told that this is just a model bias. It was over interpreted. Nobody has such sharp vision on electron density map. If this was correct, why nobody could find this and report to CCP4 within last 7 years? Eventually, a senior team member emailed to CCP4 about this issue. Since then, the definition of FMN was updated, according to my suggestion. I was asked “how did you find it?”……. “why you believed you are so right?” I really don’t how to answer. Je pense donc je suis Kevin On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley <paul.ems...@bioch.ox.ac.uk<mailto:paul.ems...@bioch.ox.ac.uk>> wrote: > On 31/03/12 23:08, Kevin Jin wrote: > > > I really wish PDB could have some people to review those important > structures, like paper reviewer. > > > So do the wwPDB, I would imagine. > > But they can't just magic funding and positions into existence... > > If the coordinate is downloaded for modeling and docking, people may not > check the density and model by themself. However this is not the worst case, > since the original data was fabricated. > > > 1. All of data was correct and real, > > > Hmmm... > > It will be very difficult for people to check the density and coordinated > if he/she is not a well-trained crystallographer. > > > I hope and believe that this is not the case. Even basically-trained > crystallographers should be able to calculate and interpret difference maps > of the kind described by Bernhard. And with the EDS and PDB_REDO server, > one does not even need to know how to make generate a difference map... > > Paul. > > -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/
