------------------------------------------------------------------------
Protein Data Bank
Quarterly Newsletter
Release #73
July 1995
------------------------------------------------------------------------
The latest version of the Electronic Deposition Form should be obtained
from the FTP /pub directory before depositing data.
------------------------------------------------------------------------
JULY 1995 PDB RELEASE
3689 full-release atomic coordinate entries
(242 new additions)
3428 proteins, enzymes, and viruses
251 nucleic acids
10 carbohydrates
365 structure factor entries
31 NMR experimental entries
The total size of the atomic coordinate entry database is 1273 Mbytes
uncompressed.
------------------------------------------------------------------------
TABLE OF CONTENTS
What is New at the PDB
PDB Browser Linked to BioMagResBank
IUCr WWW Server
A Protein Motions Database
Announcement: Call for Targets for Protein Structure Prediction
Suggestions for Filling Out the Electronic Deposition Form
� Features of Deposition Form
� Null Values
� Author Names
� Residue Name and Chain Identifier
� Sequence Number and Insertion Code
� Continued Lines
� Repeating Blocks
� PDB Entries
Good-bye to John Skora
The Portable WWW Browser
� The Browser Code
� The Search Engine
� File Service
Accessing Individual PDB Entries via the WWW
3DBbase � A Relational Database
Access to PDB
� World Wide Web (WWW)
� Gopher
� FTP
� Listserv
Order Form
Affiliated Centers
------------------------------------------------------------------------
WHAT IS NEW AT THE PDB
The Protein Data Bank (PDB) at Brookhaven National Laboratory
(BNL) is an archive of experimentally determined three dimensional
structures of biological macromolecules, serving a global community
of researchers, educators, and students. The challenges presented by
the enormous growth in data over the past several years have been met
by the PDB staff and management, which now provide an up-to-date
archive while simultaneously expanding network access and building
strong worldwide collaborations with related databases and resources.
Even larger challenges are at hand, as the deposition rate continues
to rise along with the expectations of the consumers of these data.
We are enhancing the capabilities of the PDB and transforming it into
a new biological Three-Dimensional Macromolecular Structure Database
while at the same time retaining many of the features of the PDB, for
compatibility purposes.
Over the course of the next few years, we plan to:
- Ensure that the archive remains current, accurate, and relevant;
- Provide a rapid and painless automated deposition system, using
internationally agreed-upon standards;
- Enhance data validation tools;
- Build a relational database to store and provide flexible access
to the information;
- Integrate the PDB with complementary biological and chemical
databases through semantic links and schema sharing;
- Provide easy access, through the Internet, to the PDB at BNL
and other deposition and distribution sites worldwide.
� Joel L. Sussman
------------------------------------------------------------------------
PDB BROWSER LINKED TO BIOMAGRESBANK
The PDB and BioMagResBank (BMRB), a data bank of NMR chemical shift
information for over 400 proteins and peptides, have initiated a joint
collaboration. Users can now retrieve BMRB entries containing chemical
shift information - corresponding to PDB entries for the identical
structures obtained using the PDB's WWW browser - by means of hyperlinks
inserted automatically into the retrieved PDB entries by the browser.
In the future, BMRB entries additionally will contain proton-exchange,
order parameter, coupling constant, and other kinetic and thermodynamic
data derived by NMR spectroscopy from proteins, peptides, and nucleic
acids. As the BMRB and PDB databases expand, additional links will be
established between complementary sets of data. BMRB is located at the
University of Wisconsin-Madison and is supported by a grant from the
National Library of Medicine.
------------------------------------------------------------------------
IUCR WWW SERVER
The International Union of Crystallography (IUCr) has a home page on
WWW reachable with the URL http://www.iucr.ac.uk/welcome.html. It
includes information about the Union, journals, CIF, forthcoming
meetings, and pointers to other sources of information.
Of particular utility is the World Database of Crystallographers that
can now be accessed on-line either through a form if your WWW server
(e.g. Mosaic, Netscape) supports forms or by gopher. You no longer need
to have a printed copy on your desk. This database is being updated
regularly.
There is information on the IUCr home page on how to get the most out
of all these services. If you don't have direct Internet access, send
an e-mail message to cif@iucr.ac.uk consisting of the following: send
howto.asc. Be sure absolutely nothing else appears in the body of the
e-mail, not even your signature or the period after the word `asc'. You
will receive a complete description of information services supplied by
the Union and available through e-mail.
------------------------------------------------------------------------
A PROTEIN MOTIONS DATABASE
This article was written by Mark Gerstein, Dept. of
Structural Biology, Stanford Univ., Stanford, CA, USA.
We have created a database describing protein motions, arranged
around a multi-level classification scheme including domain motions,
loop motions, and subunit motions. In addition to listing relevant
proteins and descriptions of their motion, the database contains
pictures of the motion and hypertext links to journal articles
and molecular coordinates. It is accessible via Internet using
WWW with the following URL: http://hyper.stanford.edu/~mbg/ProtMotDB/.
It is also accessible via anonymous FTP with the following URL:
ftp://hyper.stanford.edu/pub/mbg/ProtMotDB/ProtMotDB.raw.txt.
Using the database is very easy. You access its main page with one of
the popular WWW browsers such as Mosaic or Netscape. You can type
various keywords into this page and the database will display the
entries for the relevant protein motions. Finally, you can click on
various highlighted words in these entries, and this, in turn, will
either link you directly to a relevant Medline abstract from the
journal literature or bring up pictures and movies showing the protein
motion.
[In order to view movies, pictures, postscript files, etc. you may have
to build, and make your browser aware of, auxiliary applications. You
can obtain information on how to do this for the two most popular
browsers at http://home.netscape.com/eng/mozilla/1.1/faq.html and
http://www.ncsa.uiuc.edu/SDG/Software/XMosaic/mosaic-faq.html, each of
which can be easily accessed from the help menus of Netscape and Mosaic.]
The protein motions database should be of use to the community of
biologists and biochemists because it collects information about
many different kinds of motions in one place. This can greatly
facilitate comparative analyses, for example. These data are
particularly relevant at present because of the large and exponentially
increasing number of solved protein structures (currently estimated at
three thousand and increasing by about one per day). Furthermore, the
graphical and interactive nature of the database is well-suited for
the understanding of protein motions, which are often difficult to
represent on a printed page. This is particularly important because
many published papers about interesting protein motions do not
precisely describe the relationship between the motion and specific
publicly-accessible coordinate files and viewing orientations. For
example, many papers do not tell you that the atomic coordinates for
the open form are available as PDB entry 1ABC and those for the closed
form are PDB entry 2ABC and that the motion is best viewed when looking
down the crystallographic three-fold after fitting residues 5 to 90.
The database attempts to cover all instances of protein motion for which
there is at least some structural information. The classification scheme
is an expanded version of the one described previously; see M. Gerstein,
A. Lesk, C. Chothia, Structural Mechanisms for Domain Movements in
Proteins, Biochemistry 33, 6739-6749 (1994).
- The basic division of items in this database is according to
these three categories - loop and fragment motions, domain
motions, and subunit motions. Within each category the motions
are ranked according to the size of the entity that is moving.
- The next division is on the basis of available information such
as whether structures of two conformations (e.g. open and closed)
are known from crystallography or NMR, or is only one conformation
known and the other suggested on the basis of other evidence?
- The final division is on the basis of mechanism. The motion is
classified according to whether it involves rotation about
distinct hinges or pivots, incremental sliding motions of
different parts of the protein against each other (shear motions),
partial refolding, or an allosteric transition.
Originally, the information associated with each protein was basic - its
location in the classification described above, a brief text description
of the motion, the PDB ident codes of the conformations (if available),
and the references to the papers describing the motions. As the database
project has progressed, more and more information has been added to each
entry. Some entries, for instance, now have links to simple pictures and
even movies (in MPEG format). The PDB ident codes associated with each
entry have been made into hypertext links pointing directly to the
structure entries at the Brookhaven PDB, to sequence and journal cross-
references via the National Center for Biotechnology Information's
(NCBI) Entrez database, and to a listing of related structures via the
SCOP Database (see the January 1995 PDB Newsletter). Some of the
references have also been directly linked to the corresponding Medline
abstracts. The transformations and residue selections needed to
optimally superimpose and orient each coordinate set to view the motion
are provided with each entry. A WWW form linked to this database is
provided for submitting entries.
For comments or additional information please contact Mark Gerstein at
mbg@hyper.stanford.edu.
------------------------------------------------------------------------
ANNOUNCEMENT: CALL FOR TARGETS FOR PROTEIN STRUCTURE PREDICTION
IRBM (Istituto di Ricerche di Biologia Molecolare)
Practical Course: Frontiers of Protein Structure Prediction
October 8 - 17, 1995; Pomezia, Rome, Italy
Organizers: T. Hubbard (CPE, MRC), A. Tramontano (IRBM)
Instructors: G. Barton (Oxford), T. Hubbard (Cambridge),
D. Jones (London), M. Sippl (Salzburg), A. Valencia (Madrid)
Lecturers: A. Lesk (Cambridge), J. Moult (Rockville),
B. Rost (Heidelberg), C. Sander (Cambridge)
The aim of this workshop is to predict as much as possible about the
structure of a number of proteins of biological interest, taking
advantage of the most recent methodologies for fold recognition and
ab initio prediction.
If you are interested in a structure prediction being made for a
protein which does not appear to be homologous to any known structure
and for which there is no sign of an experimental structure being
determined, please consider submitting it as a target for this course.
The predictions will be made public as a technical document and also
available via WWW.
For further information and on-line target submission forms see
http://www.mrc-cpe.cam.ac.uk/predict/.
------------------------------------------------------------------------
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Incorrect
---------
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chain identifier A
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free R value : 0.021
free R value :
Incorrect
---------
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free R value : -----
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Correct
-------
author(s): J.L.Sussman,S.R.Holbrook,R.W.Warrant,
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Incorrect
---------
author(s): JL Sussman,SR Holbrook,RW Warrant,GM
Church,S-H Kim.
� Residue Name and Chain Identifier
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Correct
-------
residue name : N
chain identifier :
residue name : ASN
chain identifier : A
residue name : adenosine
chain identifier : A
residue name : GLY SER ASN GLY MET
chain identifier : A
residue name : GSNGM
chain identifier : A
Incorrect
---------
residue name : ASN A
chain identifier :
residue name : GLY 27 A--> MET 31 A
chain identifier :
residue name : from GLY 27 A TO MET 31 A
chain identifier :
� Sequence Number and Insertion Code
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Correct
-------
sequence number : 84
insertion code : A
sequence number : 84,85,86
insertion code : A
sequence number : 84 - 120
insertion code :
sequence number : 84 - 120, 130 - 150
insertion code :
Incorrect
---------
sequence number : thr 84
insertion code :
sequence number : 84A
insertion code :
� Continued Lines
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Correct
-------
remark: This model is one of two independently refined models of
the reduced SOD structure. Comparison of the two models was used
to analyze coordinate errors and water structure. The other model,
as well as the final model, obtained after combining the two
corresponding structure factor data sets, can also be found in
this database.
Incorrect
---------
remark: This model is one of two independently refined models of
remark: the reduced SOD structure. Comparison of the two models
remark: was used to analyze coordinate errors and water structure.
remark: The other model, as well as the final model, obtained
remark: after combining the two corresponding structure factor
remark: data sets, can also be found in this database.
Incorrect
---------
remark: This model is one of two independently refined models of
the reduced SOD structure. Comparison of the two models
was used to analyze coordinate errors and water structure.
The other model, as well as the final model, obtained
after combining the two corresponding structure factor
data sets, can also be found in this database.
� Repeating Blocks
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TERMINAL RESIDUE (TER)
// \\
residue name : LYS
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sequence number : 18
insertion code :
\\ //
// \\
residue name : CYS
chain identifier : L
sequence number : 219
insertion code :
\\ //
// \\
residue name : ARG
chain identifier : H
sequence number : 220
insertion code :
\\ //
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Example of how to insert correctly-formatted PDB records:
HELIX (optional, see box above)
Give inclusive pairs of residues to define each helical
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(text omitted)
determination method :
// \\
helix identifier :
helix class :
remark :
initial chain id [ ] seq number [ ] insert code [ ]
terminal chain id [ ] seq number [ ] insert code [ ]
\\ //
HELIX 1 1 ALA L 80 ASP L 82 5
HELIX 2 2 SER L 122 THR L 126 1
HELIX 3 3 LYS L 183 GLU L 187 1
HELIX 4 4 PHE H 29 ASN H 31 5
HELIX 5 5 LYS H 73 SER H 75 5
HELIX 6 6 SER H 84 ASP H 86 5
HELIX 7 7 ASN H 162 GLY H 164 5
HELIX 8 8 PRO H 213 SER H 215 5
------------------------------------------------------------------------
GOOD-BYE TO JOHN SKORA
We would like to sincerely thank John Skora for his five years of
dedication and hard work with the PDB as our Systems Manager. John
has decided to leave the PDB for another position. Our very best
wishes to him in the future.
John McCarthy will be taking over John Skora's responsibilities, and
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Mr. McCarthy has been with the PDB for five years and looks forward to
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should now go to John McCarthy at mccarthy@bnl.gov.
------------------------------------------------------------------------
THE PORTABLE WWW BROWSER
The WWW version of the PDB browser has met with success in many areas of
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Since this version of the browser uses the WWW, Dave Stampf, in
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In order to run the WWW browser locally, you have to be running
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Once you have a system with a functional http server and Perl,
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� The Browser Code
The first layer is a Perl script and its associated help file. This
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In order to perform the installation, you need to edit between one and
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� The Search Engine
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� File Service
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To install the third layer, you simply need to identify the location of
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All of the files necessary to install the portable WWW browser,
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Dave Stampf (drs@bnl.gov).
------------------------------------------------------------------------
ACCESSING INDIVIDUAL PDB ENTRIES VIA THE WWW
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In order to distribute the network load evenly around the globe, we
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------------------------------------------------------------------------
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This database development work is a collaboration that includes the
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We plan to have a fully operational database system by October 1995. In
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------------------------------------------------------------------------
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AFFILIATED CENTERS
Twenty-two affiliated centers offer DATAPRTP information for distribution.
These centers are members of the Protein Data Bank Service Association
(PDBSA). Centers designated with an asterisk(*) may distribute DATAPRTP
information both on-line and on magnetic or optical media; those without
an asterisk are on-line distributors only.
BMERC
BioMolecular Engineering Research Center
College of Engineering, Boston University
Boston, Massachusetts
Nancy Sands (617-353-7123)
sands@darwin.bu.edu
http://bmerc-www.bu.edu/
*BIOSYM
BIOSYM Technologies, Inc.
San Diego, California
Rick Lee (619-546-5536)
rickl@biosym.com
http://www.biosym.com/
BIRKBECK
Crystallography Department
Birkbeck College, University of London
London, United Kingdom
Alan Mills (44-171-6316810)
a.mills@cryst.bbk.ac.uk
http://www.cryst.bbk.ac.uk/PDB/pdb.html/
CAN/SND
Canadian Scientific Numeric Data Base Service
Ottawa, Ontario, Canada
Roger Gough (613-993-3294)
cansnd@vm.nrc.ca
CAOS/CAMM
Dutch National Facility for Computer Assisted Chemistry
Nijmegen, The Netherlands
Jan Noordik (31-80-653386)
noordik@caos.caos.kun.nl
http://www.caos.kun.nl/
*CCDC
Cambridge Crystallographic Data Centre
Cambridge, United Kingdom
David Watson (44-1223-336394)
dgw1@chemcrys.cam.ac.uk
CSC
CSC Scientific Computing Ltd.
Espoo, Finland
Heikki Lehvaslaiho (358-0-457-2076)
heikki.lehvaslaiho@csc.fi
http://www.csc.fi/
CINECA
NE Italy Interuniversity Computing Center
Casalecchio di Reno (BO), Italy
Laura Setti (39-51-6599478)
asltc0@icineca.cineca.it
ICGEB
International Centre for Genetic Engineering and Biotechnology
Trieste, Italy
Sandor Pongor (39-40-3757300)
pongor@icgeb.trieste.it
EMBL
European Molecular Biology Laboratory
Heidelberg, Germany
Hans Doebbeling (49-6221-387-247)
hans.doebbeling@embl-heidelberg.de
http://www.EMBL-Heidelberg.DE/
INN
Israeli National Node
Weizmann Institute of Science
Rehovot, Israel
Leon Esterman (972-8-343934)
lsestern@weizmann.weizmann.ac.il
*JAICI
Japan Association for International Chemical Information
Tokyo, Japan
Hideaki Chihara (81-3-5978-3608)
*MAG
Molecular Applications Group
Palo Alto, California
Hilary Jensen (415-473-3039)
hilary@suerte.mag.com
http://hyper.stanford.edu/~Mag/
*MSI
Molecular Simulations Inc.
Burlington, Massachusetts
Lance J. Ransom Wright (617-229-9800)
lance@msi.com
http://www.msi.com/
NCHC
National Center for High-Performance Computing
Hsinchu, Taiwan, ROC
Jyh-Shyong Ho (886-35-776085; ex: 342)
c00jsh00@nchc.gov.tw
NCSA
National Center for Supercomputing Applications
University of Illinois at Urbana-Champaign
Champaign, Illinois
Patricia Carlson (217-244-0768)
pcarlson@ncsa.uiuc.edu
NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION
National Library of Medicine
National Institutes of Health
Bethesda, Maryland
Stephen Bryant (301-496-2475)
bryant@ncbi.nlm.nih.gov
http://www.ncbi.nlm.nih.gov/
*OML
Oxford Molecular Ltd.
Oxford, United Kingdom
Steve Gardner (44-1865-784600)
sgardner@oxmol.co.uk
http://www.oxmol.co.uk/
*OSAKA UNIVERSITY
Institute for Protein Research
Osaka, Japan
Yoshiki Matsuura (81-6-879-8605)
matsuura@protein.osaka-u.ac.jp
PITTSBURGH SUPERCOMPUTING CENTER
Pittsburgh, Pennsylvania
Hugh Nicholas (412-268-4960)
nicholas@psc.edu
http://pscinfo.psc.edu/biomed/biomed.html/
SEQNET
Daresbury Laboratory
Warrington, United Kingdom
User Interface Group (44-1925-603351)
uig@daresbury.ac.uk
*TRIPOS
Tripos, Inc.
St. Louis, Missouri
Akbar Nayeem (314-647-1099; ex: 3224)
akbar@tripos.com
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Protein Data Bank
Chemistry Department, Bldg. 555
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000 USA
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TO CONTACT PDB
Telephone.....516-282-3629
Facsimile.....516-282-5751
Internet:
pdb@bnl.gov....................general correspondence
orders@pdb.pdb.bnl.gov.........order information
sysadmin@pdb.pdb.bnl.gov.......network services
listserv@pdb.pdb.bnl.gov.......Listserver subscriptions
pdb-l@pdb.pdb.bnl.gov..........Listserver postings
errata@pdb.pdb.bnl.gov.........entry error reporting
Please include your name, postal mailing address, e-mail address,
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STATEMENT OF SUPPORT
PDB is supported by a combination of Federal Government Agency
funds (work supported by the U.S. National Science Foundation;
the U.S. Public Health Service, National Institutes of Health,
National Center for Research Resources, National Institute of
General Medical Sciences, and National Library of Medicine; and
the U.S. Department of Energy under contract DE-AC02-76CH00016)
and user fees.
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PDB STAFF
Joel L. Sussman, Head
David R. Stampf, Sr. Project Mgr.
Enrique E. Abola, Science Coordinator
Jaime Prilusky, Interim Head Database Dev.
Frances C. Bernstein
Judith A. Callaway
Minette Cummings
Betty R. Deroski
Pamela A. Esposito
Arthur Forman
Patricia A. Langdon
Michael D. Libeson
Nancy O. Manning
John E. McCarthy
Regina K. Shea
Karen E. Smith
Dejun Xue
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