Dear Kay and colleagues,
It is possible to extend the inspection of data associated to a PDB
entry beyond Table 1 by means of the PDBpeep server available at
http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi
Doing so for these three entries shows that while 6MO2 has a rather normal
3D distribution of <I/sd(I>) and <CC1/2>, both 6MO0 and 6MO1 show a strange
pattern for these two quantities, where the iso-surfaces are pinched towards
the origin along the c* axis - perhaps, indeed, an indication that the space
group is wrong and that the point group is 3 rather than 32 (?). It might be
something else, but there is a definite anomaly in the 3D distributions of
these two statistics.
With best wishes,
Gerard.
--
On Fri, Jul 19, 2019 at 06:07:33PM +0100, Kay Diederichs wrote:
> Hi Tristan et al,
>
> before people invest their time into re-refining a model against the
> deposited data, I'd suggest that these data are dubious - see table S3 in
> https://pubs.acs.org/doi/suppl/10.1021/jacs.9b02505/suppl_file/ja9b02505_si_001.pdf
> ! The data processing statistics look "surprising" to me: "Rsym or Rmerge"
> values are unexpectedly high, and the high-resolution cutoffs for 2 of the 3
> structures are too low. Maybe the space group is wrong? With such data,
> ligand density cannot expected to be meaningful, I'd say.
> In my eyes, the authors should be asked for the raw data images, and these
> should be reprocessed before re-refinement.
>
> best,
> Kay
>
> On Fri, 19 Jul 2019 17:05:21 +0100, Tristan Croll <ti...@cam.ac.uk> wrote:
>
> >I couldn't resist doing a little playing with 6mo0 in ISOLDE. The
> >sequence past Gly1151 is wrong - after jumping a small gap (density
> >clearly indicates a single missing residue here), it continues on from
> >1165. Corrected the following sequence to GVVTRS, deleted the ligands,
> >did some basic energy minimisation and cleaning up of obvious local
> >problems, reset the B-factors and refined in Phenix.refine. Rwork/Rfree
> >28/32, MolProbity score 2.14 (vs. 3.6 originally). No sign of anything
> >like the ligand in the difference density (just a small blob in the
> >active site). Some other oddities make me suspect a number of point
> >mutations from the assigned sequence (not register errors - the
> >surrounds are quite clear). I'm particularly intrigued by residues 48-71
> >- this stretch appears to link seamlessly head-to-tail with its own
> >symmetry copy, forming a seemingly-continuous chain snaking through the
> >crystal. Can't make head nor tail of that. A decidedly odd structure...
> >but I agree with you that the ligand doesn't seem supported by the
> >density.
> >
> >Best regards,
> >
> >Tristan
> >
> >On 2019-07-19 14:46, herman.schreu...@sanofi.com wrote:
> >> Hi Rhys,
> >>
> >> There is definitively some density present for a ligand, but the
> >> active site region looks completely misfitted, and the ligand density
> >> may also belong to unfitted protein residues. One first needs to get
> >> the protein chain right, and should then look if there would still be
> >> density available to fit the ligand.
> >>
> >> Best,
> >>
> >> Herman
> >>
> >> VON: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] IM AUFTRAG VON
> >> Rhys Grinter
> >> GESENDET: Freitag, 19. Juli 2019 15:22
> >> AN: CCP4BB@JISCMAIL.AC.UK
> >> BETREFF: [EXTERNAL] [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1,
> >> 6MO2
> >>
> >> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
> >>
> >> Hi All,
> >>
> >> I was chatting with a colleague during a recent synchrotron visit and
> >> they'd recently come across some ligand/drug bound structures
> >> associated with a paper recently published in a high impact factor
> >> journal.
> >>
> >> They had pulled the associated SFs from the PDB and found that the
> >> electron density associated with these ligands didn't match that
> >> reported in the paper and certainly wasn't sufficient to model the
> >> alleged ligand.
> >>
> >> I also pulled the structure factors and after refinement in the
> >> presence/absence of the alleged ligand I also feel that the density
> >> present does not warrant modelling of the ligand.
> >>
> >> I was hoping that the community might be able to give me an outside
> >> opinion on these datasets (PDB IDs: 6MO0, 6MO1, 6MO2) and if the
> >> problem associated with the data is verified, provide some advice on
> >> how to proceed.
> >>
> >> This isn't the first occasion I've seen ligand bound structures with
> >> questionable density deposited in association with papers in well
> >> respected journals. Despite improvements to validation I feel that
> >> this problem is widespread.
> >>
> >> Best Regards,
> >>
> >> Rhys
> >>
> >> --
> >>
> >> Dr Rhys Grinter
> >>
> >> NHMRC Postdoctoral Researcher
> >>
> >> Monash University
> >>
> >> +61 (0)3 9902 9213
> >>
> >> +61 (0)403 896 767
> >>
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