http://trololololololololololo.com/
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/
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
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