Dear Kevin et al.,
At the risk of being flamed as well, I could not resist this opportunity for
shameless self promoting.... During my Ph.D. I worked on a flavoprotein as well
and found flavin bending angles of 10 and 19°. I even published pictures of the
electron density of the flavin (J.Mol.Biol.(1989), 208:679-696) and cited a
reference from 1987 reporting a flavin bending angle of 20° for another
flavoprotein. In this time, one had to presonally modify the PROLSQ restraints
by hand, since if something was defined as being flat, it would become flat, no
matter what the electron density was trying to say. "Trying" since there was no
Rfree, no maximum likelyhood refinement and no CCP4BB so the maps were heavily
biased.
Although this period is commonly referred to as the stone-age of protein
crystallography, many crystal structures were solved in this time that are
still valid today. Before reinventing wheels, one could look a little further
back in the literature than the last 7 years. Remains the question how this
incorrect FMN definition could remain in the CCP4 package for so long. We need
more people like Kevin, who loudly complain about errors in the CCP4
definitions instead of just fixing one's personal definition.
Cheers!
Herman
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Kevin Jin
Sent: Sunday, April 01, 2012 9:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
"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/
