Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis.
============================ David C. Briggs PhD Father, Structural Biologist and Sceptic ============================ University of Manchester E-mail: david.c.bri...@manchester.ac.uk ============================ Webs : http://flavors.me/xtaldave Twitter: @xtaldave Skype: DocDCB ============================ On 1 April 2012 21:27, Kendall Nettles <knett...@scripps.edu> wrote: > What is the single Latin word for troll? > > Kendall > > On Apr 1, 2012, at 3:06 PM, "Kevin Jin" <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> > 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/ > > >
