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[ccp4bb]: Problems with PDB entry 1muo
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Dear colleagues,
This is not actually a question but a petition that concerns
crystallography, or more accurately, the public availability of
crystallographic data.
Background:
On March 28 I tried to fetch from the PDB the coordinates of a kinase
whose structure was published in the Journal of Biological Chemistry the
last November. It has ID, 1muo.
"Crystal structure of aurora-2, an oncogenic serine/threonine kinase"
Cheetham GM, Knegtel RM, Coll JT, Renwick SB, Swenson L, Weber P, Lippke
JA, Austen DA.
J Biol Chem. 2002 Nov 8;277(45):42419-22.
In this paper you can read:
"The atomic coordinates and structure factors (code 1MUO) have been
deposited in the Protein Data Bank, Research Collaboratory for
Structural Bioinformatics, Rutgers University, New Brunswick, NJ
(http://www.rcsb.org/)."
The "Instruction to Authors" from the Journal of Biological Chemistry
(http://www.jbc.org/misc/ifora.shtml) states:
"Crystallographic Studies
Authors of papers describing new structure determinations must submit to
the Protein Data Bank at Research Collaboratory for Structural
Bioinformatics http://www.rcsb.org/pdb all structural data required to
validate the conclusions, including both x-ray amplitudes and phases and
the derived atomic coordinates. JOURNAL policy requires that such data
be available upon request IMMEDIATELY after publication (...)"
Facts:
1. There is a 1muo entry in the PDB with the right title and authors,
but:
1.1. This entry doesn't include the structure factors, only coordinates.
1.2. This entry ins "ON HOLD" until 24 September 2003.
2. When I contacted the PDB asking them to release the coordinates,
according to the journal policies, they told me that they were in
contact with the author to do so, and they encouraged me to write the
author as well.
3. I wrote to Dr. Cheetham on March 31. No answer yet.
4. I wrote to the Journal of Biological Chemistry on April 2. They wrote
as well to Dr. Cheetham.
5. The coordinates are still "on hold" and no structure factors have
been deposited (April 7).
Discussion:
I've been adviced that the PDB has no authority to release data without
the authors' consent. The journal, of course, has not this authority
either.
I don't know yet what happened in this particular case. There may be a
reasonable explanation for the author not remembering to instruct the
PDB to release the coordinates, and not answering now our emails.
But, what can we do to avoid this happening? It is not honest or
responsible to publish an article in a journal with the clear
requirement of releasing coordinates and data, and then not to do
so. Otherwise, anybody following the rules will be at big disadvantage
with respect of people failing to do so.
Petition:
Please email me with details of any other abuses of journal policies of
which you are aware. I feel that only through publicity and public
complaints will the avowed policy of immediate release after publication
of coordinates and the deposition of the corresponding structure factors
be achieved.
Thank you for your attention.
Cheers,
Miguel
PS: Please, excuse me if you receive this email more than once.
--
Miguel Ortiz Lombardía
email: mol@ysbl.york.ac.uk
http://www.ysbl.york.ac.uk/~mol
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