The PDB has a New Home
On Oct. 1, 1998 the Research Collaboratory for Structural Bioinformatics
(RCSB), a consortium composed of Rutgers, the State U. of New
Jersey; U. of California San Diego/San Diego Supercomputer Center
(SDSC); and the National Inst. of Standards and Technology (NIST),
received a five-year award to manage the Protein Data Bank (PDB).
The project will run under a Cooperative Agreement from the National
Science Foundation (NSF), with funding from that agency as well
as the Dept. of Energy, and two units of the National Institutes
of Health: the National Inst. of General Medical Sciences and
the National Library of Medicine.
The RCSB has created a system with higher, faster throughput
of deposited data; a greater number of query capabilities, including
more complex and specific queries; a uniform archive; dynamic
cross-links to other databases; and the availability of structure
and sequence neighboring. The PDB data will be stored and mirrored
at all three RCSB sites and at key sites worldwide.
Principal investigator H. Berman heads the RCSB team at Rutgers
which includes J. Westbrook, who has played a key role in the
development of the mmCIF dictionary. At the San Diego Supercomputer
Center (SDSC) at UCSD, P. Bourne leads a group of scientists
in a Biological Data Representation and Query initiative. Together
with P. Arzberger, a computational biologist and Executive Director
of NPACI, this group will be responsible for all aspects of data
query and distribution. G.L. Gilliland, chief of the Biotechnology
Div. in NIST's Chemical Science and Technology Lab, will lead
the NIST effort to establish data uniformity, improve the accessibility
and reliability of queries, and manage the Master Archive.
The RCSB is working with the Brookhaven National Laboratories
(BNL) team headed by J. Sussman to ensure that there is a seamless
transition that will be completed by Oct. 31, 1999. A website
(http://www.rcsb.org) has
been established to provide up to date transition information
and to provide access to the new features of the system as they
become available.
Helen Berman, Gary Gilliland, Phil Bourne
From ACA Newsletter
International Collaboration
Grants are available to individual American specialists who plan
to establish new research partnerships with their colleagues
from Central/Eastern Europe (CEE) and the Newly Independent States
(NIS). This program is designed primarily to prepare these new
partnerships for competition in NSF programs. Two types of grants
are available. Short-term: to support American specialists who
wish to host or visit their CEE or NIS colleagues for two-week
periods in order to prepare collaborative research proposals
for submission to NSF. Long-term: visits last from one to six
months and significant joint publications are expected. Postmarking
deadlines for proposals are April 5, 1999 (project development
only), July 30, 1999 (long-term only) and Aug. 16, 1999 (project
development only). For more information contact http://www2.nas.edu/oia/22da.html
Teaching Tools: Lab Manual for Shelxtl
A step by step guide to solving routine crystal structures for
crystallographic novices and is entitled "Allen Hunter's
Youngstown State University X-Ray Structure Analysis Lab Manual:
A Beginner's Introduction" is available free of charge as
a .pdf file to academic users who will only be required to register
their copies and keep me informed of how it is used in their
teaching. If you are interested in obtaining a copy, please contact
me at adhunter@cc.ysu.edu.
Allen Hunter
ICSD
ICSD is now cooperatively produced by FIX Karlsruhe, the Max-Planck
Society (MPG) and the US Nat'l Inst. For Science and Tech. (NIST).
At present, the distribution of the tasks between the three partners
is as follows: ·production, distribution and marketing
by FIZ Karlsruhe, ·quality control by MPG, ·development
of new inhouse and other software as well as evaluation by NIST.
On the Cover:
Clockwise beginning at upper left:
1) Ribbon drawing of FepA, an active transporter of ferric enterobactin
in the outer membrane of E. coli. S.K. Buchanan et al. (1999)
Nature Structural Biology 6:56. Courtesy of Hans Deisenhofer,
2) Neutron quasi-Laue diffraction pattern from tetragonal hen
egg-white lysozyme revealed 960 hydrogen atoms and 251 water
molecules. N. Niimura, et al., Nature Structural Biology, Vol.4,
No11, 1997, pp909-914. Courtesy of N. Niimura; 3) Anisotropic
Displacement Parameters (ADP) of anthraquinone between 160 and
300K (Brock and Fu, Acta Cryst. B54 (1998) 308) shows butterfly-type
motion of the molecule (S.C. Capelli, Ph.D. thesis, U. of Bern,
Switzerland, 1999). Picture by J. Hauser. Courtesy of H.-B Bürgi;
4) A 24-nucleotide RNA enzyme, Leadzyme, complexed with Sr(H2O)3(II)
at 1.8 Å resolution reveals how small ribozymes recruit
metals to activate specific 2'-hydroxyl groups for nucleophilic
attack leading to phosphodiester scission. The substrate has
a purple electron density surface and yellow nucleotide bonds.
The ribozyme, a yellow electron density surface and pink nucleotide
bonds. Courtesy of David McKay; 5) The hydrate of 18-crown-6/methylammonium
fluoride, a channel structure in which water molecules form a
'double helix' along the crystallographic z axis. Courtesy of
Janusz Lipkowski; 6) A model of a surfactant templated silicate
structure at the air water interface of a cetyl trimethyl ammonium
solution being studied by X-ray and neutron reflectivity. Courtesy
of John White; 7) A very-large-pore high-silica zeolite UTD-1
bis(pentamethylcyclopentadienyl)cobalt(III) complex solved ab
initio from powder diffraction data collected on a textured sample.
Courtesy of Lynne B. McCusker; 8) The end of the myosin power
stroke from crystal structure analysis of actin and myosin and
electron microscopy of the actin-myosin complex. Courtesy
of Ken Holmes.
