Nice pick-up on the cis bond! Trp154-Trp155, correct?
On 2016-09-10 01:31, Robbie Joosten wrote:
> Hi Randy,
>
> That was brilliant (as was Gerard's decision to make the problem
> public). I agree with Manfred that this should be relayed to the
> authors and the editor of the journal. The model you posted is
> obviously something that should replace the current PDB entry 5gnn.
> I couldn't resist to have a play with your model. When you throw it
> into PDB_REDO as-is you end up with R-free already at 23.9%. If you
> add the missing 4 terminal residues before, that R-free goes down to
> 22.1%. The output from that job is at
> www.cmbi.ru.nl/pdb_redo/upload/5gnn_randy_redo.tar.gz. There is still
> much more to do for the authors to make the model good. I wanted to
> say publishable, but apparently it already was when it was still
> grossly incorrect :(
> For the validators: there is a very nice non-Pro cis-peptide if you
> fix the model manually a bit more.
>
> Cheers,
> Robbie
>
>
>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>> Manfred S. Weiss
>> Sent: Friday, September 09, 2016 13:40
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] Another puzzle: 5gnn: SOLVED
>>
>>
>> Good job Randy!
>>
>> Now, in order to finish this off properly somebody should refine the
>> structure, alert the editor of the journal as well as the
>> corresponding author
>> of the paper.
>>
>> If we leave it at that, the only thing we have is the satisfaction
>> that we
>> managed to "peer review" this structure, but nothing else is going to
>> happen.
>>
>> Cheers, Manfred
>>
>>
>> On 09.09.2016 13:34, Gerard Bricogne wrote:
>> > Dear Randy,
>> >
>> > Congratulations for this terrific piece of work!
>> >
>> > As James Fraser was writing two days ago, this case establishes a
>> > new paradigm for the "peer review" of structural papers :-) .
>> >
>> >
>> > With best wishes,
>> >
>> > Gerard.
>> >
>> > --
>> > On Fri, Sep 09, 2016 at 12:20:53PM +0100, Randy Read wrote:
>> >> Dear all,
>> >>
>> >> Following on from Paul’s suggestion that the space group is wrong, I
>> thought it might be interesting to try to solve this structure from
>> scratch,
>> using what I’m currently teaching students at a CCP4 workshop. What
>> worked was to find some distant homologues with HHpred (top 3 hits
>> after
>> ignoring 5gnn), make a trimmed ensemble, and search with that. This
>> gave a
>> very clear solution for one molecule in P65. Model completion from
>> that
>> point works really well, given the resolution, using either
>> phenix.autobuild or
>> ARP/wARP.
>> >>
>> >> For the edification of the members of the BB, the ARP/wARP model is
>> attached! (Hopefully no flames for an attachment of 135kB…) This
>> model
>> hasn’t had some really obvious rotamer fixes or extensions of the
>> termini
>> applied, but it has good stereochemistry, and R/Rfree are 0.241/0.285.
>> >>
>> >> Given the vastly improved statistics for a different space group and the
>> huge differences in the model, it is to be hoped that the authors
>> retract the
>> original publication and PDB entry. Thanks to Gerard for pointing out
>> the
>> issues with this!
>> >>
>> >> Best wishes,
>> >>
>> >> Randy Read
>> >>
>> >
>> >
>> >>
>> >>
>> >> -----
>> >> Randy J. Read
>> >> Department of Haematology, University of Cambridge
>> >> Cambridge Institute for Medical Research Tel: +44 1223 336500
>> >> Wellcome Trust/MRC Building Fax: +44 1223 336827
>> >> Hills Road E-mail: [log in to unmask]
>> >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>> >>
>> >>> On 7 Sep 2016, at 16:51, Paul Adams <[log in to unmask]> wrote:
>> >>>
>> >>> Dear Gerard,
>> >>>
>> >>> thanks for pointing this structure out. This is indeed very startling. The
>> paper indicates that the structure was refined with Phenix. However,
>> if I
>> download the model/data and refine (with Phenix) the starting
>> R-factors are
>> 0.36/0.38 and these get worse during refinement. Clearly the deposited
>> model is not consistent with the R-factors reported in the paper, or
>> in the
>> wwPDB. In addition, analysis of the data suggests strongly that the
>> true
>> symmetry is P6 (possibly with a screw axis) - I suspect that this is
>> the genesis
>> of statements about twinning, but it isn’t clear if that was used in
>> the
>> refinement. Being charitable I can imagine that the wrong model was
>> deposited in the wwPDB. However, this doesn’t explain the R-factors
>> reported by the wwPDB, or the less than convincing images of the
>> structure
>> shown in the paper. I very much agree with you that there must have
>> been
>> ample alarms sounded along the way. It is cautionary that this wasn’t
>> caught
>> at some point. For me this highlights that the issues go beyond the
>> naivety or
>> impatience of a single student.
>> >>>
>> >>> Cheers,
>> >>> Paul
>> >>>
>> >>>> On Sep 7, 2016, at 7:20 AM, Gerard Bricogne
>> <[log in to unmask]> wrote:
>> >>>>
>> >>>> Dear all,
>> >>>>
>> >>>> While the thread on "Another MR pi(t)fall" is still lukewarm,
>> >>>> and the discussion it triggered hopefully still present in readers'
>> >>>> minds, I would like to bring another puzzling entry to the BB's attention.
>> >>>>
>> >>>> When reviewing on Monday the weekend's BUSTER runs on the last
>> >>>> batch of PDB depositions, Andrew Sharff (here) noticed that entry
>> >>>> 5gnn had been flagged as giving much larger R-values when
>> >>>> re-refined with BUSTER (0.3590/0.3880) than the deposited ones
>> >>>> (0.2210/0.2500). This led us to carry out some investigation of that
>> entry.
>> >>>>
>> >>>> The deposited coordinates were flagged by BUSTER as having 4602
>> >>>> bond-length violations, the worst being 205.8 sigmas, and other
>> >>>> wild outliers. The initial Molprobity analysis gave a clash score
>> >>>> of near 100, placing it in the 0-th percentile. The PDB validation
>> >>>> report is dominantly red and ochre, with only a few wisps of green.
>> >>>>
>> >>>> Examining the model and map with Coot showed "waters, waters
>> >>>> everywhere", disconnected density, and molecules separated by large
>> >>>> layers of water. The PDB header lists hundreds of water molecules
>> >>>> in REMARK 525 records that are further than 5.0 Angs from the
>> >>>> nearest chain, some of them up to 15 Angs away.
>> >>>>
>> >>>> The cartoons on the NCBI server at
>> >>>>
>> >>>>
>> http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=142582&d
>> >>>> ps=1
>> >>>>
>> >>>> show random coils threaded up and down through beta-strands, and
>> >>>> the one on the RCSB PDB site at
>> >>>>
>> >>>> http://www.rcsb.org/pdb/explore.do?structureId=5GNN
>> >>>>
>> >>>> also shows mostly random coil, with only very few and very short
>> >>>> segments of secondary structure.
>> >>>>
>> >>>> In reciprocal space, an oddness of a different kind is that if
>> >>>> one looks at the mtz file, the amplitudes and their sigmas are on a
>> >>>> very small scale. However the STARANISO display shows a smooth and
>> >>>> plausible distribution of I/sig(I) to the full nominal resolution
>> >>>> limit of 1.6A.
>> >>>>
>> >>>> Looking at the publication associated with this entry
>> >>>>
>> >>>> http://www.ncbi.nlm.nih.gov/pubmed/27492925
>> >>>>
>> >>>> indicates that the structure was solved by MR from a model obtained
>> >>>> from a structure prediction server (I-TASSER). No further details
>> >>>> are given, even in the Supplemental Material. Table 1 does report a
>> >>>> MolProbity clash score of 103.59, as well as 10% Ramachandran
>> >>>> outliers and 25.51% rotamer outliers. It also contains a mention of
>> >>>> a twinning operator -h, -k, l with a twinning fraction of 0.5,
>> >>>> although there is no mention of it in the text nor in the PDB file.
>> >>>>
>> >>>> I will follow my own advice and resist the temptation of calling
>> >>>> this "the end of civilisation as we know it", but this is startling.
>> >>>> Perhaps we have over-advertised to the non-experts the few
>> >>>> successes of structure prediction programs as reliable sources of
>> >>>> MR models and thus created unwarranted optimism, besides the usual
>> >>>> exaggeration of the degree to which X-ray crystallography has
>> >>>> become a push-button commodity that can deliver results to
>> >>>> untrained users. What is also disconcerting is that the abundant
>> >>>> alarm bells that rang along the way (the MolProbity clash score and
>> >>>> geometry reports, the contents of the PDB validation report, and
>> >>>> simple common sense when examining electron density and model)
>> >>>> failed to make anyone involved along the way take notice that there
>> was something seriously wrong.
>> >>>>
>> >>>> This case seems to bring to the forefront even more vividly than
>> >>>> 4nl6 and 4nl7 some collective issues that we face. Here the problem
>> >>>> is not one of contamination of a protein prep resulting in crystals
>> >>>> of "the wrong protein": there is also a more diffuse contamination
>> >>>> by deficiencies of judgement, expertise and vigilance at several
>> >>>> consecutive stages, including refereeing and publication.
>> >>>>
>> >>>> Validation is a hot topic at the moment, and this may serve as a
>> >>>> concrete example that some joined-up thinking and action is indeed
>> >>>> a matter of urgency, and that extreme scenarios of things going
>> >>>> wrong do not exist solely in the imaginations of
>> >>>> obsessive-compulsive/paranoid validators.
>> >>>>
>> >>>> I am grateful to several colleagues for correspondance and
>> >>>> discussions on the matters touched upon on this message.
>> >>>>
>> >>>>
>> >>>> With best wishes,
>> >>>>
>> >>>> Gerard
>> >>>>
>> >>>> --
>> >>>>
>> >>>>
>> ==========================================================
>> =====
>> >>>> * *
>> >>>> * Gerard Bricogne [log in to unmask] *
>> >>>> * *
>> >>>> * Global Phasing Ltd. *
>> >>>> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
>> >>>> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *
>> >>>> * *
>> >>>>
>> ==========================================================
>> =====
>> >>>
>> >>> --
>> >>> Paul Adams
>> >>> Division Director, Molecular Biophysics & Integrated Bioimaging,
>> >>> Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced
>> >>> Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of
>> >>> Bioengineering, U.C. Berkeley Vice President for Technology, the
>> >>> Joint BioEnergy Institute Laboratory Research Manager, ENIGMA
>> >>> Science Focus Area
>> >>>
>> >>> Building 33, Room 347
>> >>> Building 80, Room 247
>> >>> Building 978, Room 4126
>> >>> Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul
>> >>>
>> >>> Lawrence Berkeley Laboratory
>> >>> 1 Cyclotron Road
>> >>> BLDG 33R0345
>> >>> Berkeley, CA 94720, USA.
>> >>>
>> >>> Executive Assistant: Louise Benvenue [ [log in to unmask] ][
>> >>> 1-510-495-2506 ]
>> >>> --
>>
>> --
>> Dr. Manfred. S. Weiss
>> Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular
>> Crystallography (HZB-MX) Albert-Einstein-Str. 15
>> D-12489 Berlin
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>> Email: [log in to unmask]
>>
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