RCSB PDB Newsletter #20: PDB Community Focus: Edward N. Baker

No. 20
Winter 2004


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RCSB PDB Article Published in Nucleic Acids Research

New Update Release of CD-ROM Sets

PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

PDB Community Focus: Edward N. Baker

PDB Education Corner by Katherine Kantardjieff

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© 2004 RCSB PDB


PDB Community Focus: Edward N. Baker

Edward N. Baker

Edward (Ted) N. Baker is a Professor of Structural Biology at the University of Auckland in New Zealand. He is a member of the PDB Advisory Committee, and a long-time depositor to the PDB. Following a post-doctoral fellowship with Prof. Dorothy Hodgkin, in Oxford, he joined the staff at Massey University where he initiated a protein crystallography research program by determining the structure of the kiwifruit enzyme actinidin--the first protein structure to be determined in the Southern Hemisphere, and one of the first protein structures anywhere to be refined at high resolution. He is also responsible for the first crystallographic characterization of the milk protein, lactoferrin. In 1993 he was recognized as an International Research Scholar of the Howard Hughes Medical Institute. In 1997, he was awarded the Royal Society of New Zealand's Hector Medal in recognition of his innovation and leadership in studying the relationships between protein structure and function. He has served the community as President (1996-1999) of the International Union of Crystallography (IUCr), and played a leading role in developing accepted guidelines for the deposition of macromolecular data. He was involved in the creation of Acta Crystallographica Section D and now serves as joint Editor.

The RCSB PDB interviewed Professor Baker regarding his perspective on developments in crystallography and in the PDB:

RCSB PDB: How did you become interested in crystallography and protein structure, and how have you seen this field evolve since you began?

Prof. Baker: I became interested in crystallography because I loved the idea that you could see molecules--it seemed such a clear and exciting goal. I entered protein crystallography because my wise Ph.D. supervisor steered me towards Oxford for a Postdoc. This was just after the lysozyme structure had been solved and David Phillips' group had moved to Oxford. Fred Richards was in the lab (building his Richards box--"Fred's folly"), Chris Anfinsen was visiting, Guy and Eleanor Dodson, Tom Blundell, and Vijayan were there, and the insulin structure came out. All very exciting. When I was thinking of going back to New Zealand, knowing that I wanted to do protein crystallography, and also that I would have virtually no resources, Dorothy gave me wonderful advice: "If you really want to do it, just get started and it will work out in the end." It did.

The technical changes--from a time when crystals had to be at least 0.5 mm in size, data collection took months, and we built wire models by hand--have revolutionized every aspect of the field: vastly improved crystallization methods, crystal freezing, fast data collection, synchrotrons, computer graphics (thanks to Alwyn Jones), automated methods (SOLVE!), refinement. But I think what is most exciting is the way the knowledge and use of macromolecular structure has become central to biology. No longer is protein crystallography an esoteric, if awe-inspiring, pursuit that consumed lots of money and produced remarkable understanding for a few proteins. Now it is central to drug development and it can transform a field (witness the MHC structure or the ribosome).

RCSB PDB: You were a member of the inaugural Editorial Advisory Board for Acta D and are currently joint Editor. Please tell us about the formation of Acta D, and how it has been evolving over the years.

Prof. Baker: Acta D was begun in the early 1990's in recognition of the great expansion of macromolecular crystallography that was then beginning. At that time very few of the biological journals published structural papers, though that has changed radically. In the past ten years we have seen a remarkable growth of interest in crystallographic methods, and a great period of methods development. Acta D has reflected this. The next wave is the huge increase in the numbers of experimentally-determined structures. We are already seeing large numbers of crystallization papers coming forward, and we think that these, and the structures that follow, point logically towards the establishment of a new electronic journal.

RCSB PDB: From your perspective as a both a depositor and a member of the PDB Advisory Committee: are you pleased with the current state of the PDB and what suggestions would you make as we move forward?

Prof. Baker: I am very happy with the current state of the PDB. There were concerns a few years ago as to whether the PDB could cope with the explosive growth in new structures. But I think the current speed with which new depositions are processed and released has allayed those fears. And I am also very pleased that problem of having large numbers of structures "on hold" has largely gone away--in part due to simple changes in the deposition defaults. Annotations and quality checks can always be done better, and will depend on better capturing of additional data.

What I think is the biggest challenge is to be able to make the structural data more accessible and meaningful for users. As a crystallographer I know very well which parts of my own structures are well-defined and which are not. I can assess other crystal structures quite well, too. The challenge is to express the indications that are given by data quality, electron density, B factors, occupancies, and correlation coefficients, in forms that can be intuitively understood by non-crystallographic users. Similar challenges exist for NMR structures.

RCSB PDB: Along with the MSD-EBI and the PDBj, we have just announced the formation of the Worldwide PDB (wwPDB). How do you, as a member of the international community of PDB users, view this agreement?

Prof. Baker: I applaud this unreservedly. Traditionally, crystallographers always viewed the PDB as "their" database, and viewed it as a single international resource. After all, they provided the data (this now includes NMR spectroscopists, of course). This feeling became muddied in the 1990's, around the time of the transfer of the PDB from Brookhaven to the RCSB, and one could even hear references to "the European PDB" and "the U.S. PDB". How did a New Zealander, far from both, fit in? Thankfully, this is now a thing of the past, and I hope that the right framework can now be developed for the long-term management and maintenance of this single Worldwide PDB.

The structure of actinidin--the first protein structure determined in the Southern Hemisphere.

PDB ID: 2act

E.N. Baker, E.J. Dodson (1980): Crystallographic refinement of the structure of actinidin at 1.7 Ångstroms resolution by fast Fourier least-squares methods. Acta Crystallogr., Sect. A 36, p. 559.