New Structure for PKA

Enrique Abola - BIOSCI mail biosci at PAE.PDB.BNL.GOV
Mon Mar 29 15:38:09 EST 1993

On Mar 26,  6:29pm, Jnet%\ wrote:
> Subject: Re: New Structure for PKA
> Received: From STANFORD(MAILER) by BNLDAG with Jnet id 2236
>           for ABOLA at BNLDAG; Fri, 26 Mar 1993 18:29 EST
> Received: by Forsythe.Stanford.EDU; Fri, 26 Mar 93 15:29:35 PST
> Received: by (5.65/IG-2.0)
>         id AA20310; Fri, 26 Mar 93 14:26:50 -0800
> Received: by (5.65/IG-2.0)
>         id AA20305; Fri, 26 Mar 93 14:26:46 -0800
> Message-Id: <9303262226.AA20305 at>
> To: protein-crystallography at
> From: lwalsh at nemo (Laura L. Walsh)
> Subject: Re: New Structure for PKA
> Date: 26 Mar 93 22:14:24 GMT
> Sender: usenet at (Net Noise owner)
> pettsj at (James Petts) writes:
> >I have just been reading with interest the publication reporting the
> >structure of the ternary complex of PKA, PKI, and ATP in the EMBO Journal
> >(12(3), 849, 1993). The article states that the coordinates have been
> >deposited at Brookhaven. Can anybody tell me what the PDB entry code for
> >this structure is, and if it is available for ftp yet?
> > ===> James Petts <===
> Often there is a considerable delay between the time that the
> coordinates are deposited at Brookhaven and their release.  I
> cannot find the new PKA structure in my database yet.
> Laura Walsh
>-- End of excerpt from Jnet%\

Enclosed is a copy of the latest PDB newsletter that provides information
on current turn-around time between deposition and release.  A six
week turn-around time had been achieved starting sometime in Dec. 1992 and
Jan. 1993.   We are continually improving our procedures in order that
we may have data available to the users ASAP.

The entries that James is looking for have been placed on hold for a
year by the depositors.  They will be available sometime in April 1994.

State of the PDB                                           January 1993
The Protein Data Bank (PDB) is very much a resource in
transition. In fulfilling its mission to provide the
international scientific and technological community with
access to information and knowledge on 3-D structures of
biological macromolecules, PDB is reorganizing its staff, while
developing increasingly automated procedures for data submission
and validation. New procedures for data distribution and user
access, and for maintenance of the PDB archive at Brookhaven,
also are being developed. PDB is actively planning to expand its
role as a center for coordination and development of the new
database management, manipulation and analysis tools that will
be required in the future if the rapidly growing mass of 3-D
structural information is to be effectively utilized. At the
same time PDB plans to develop a research program strongly
coupled to the database, involving application of the data for
forefront studies in structural biology.

An important milestone reached with this release brings PDB's
coverage completely up-to-date on prerelease. All prerelease
entries have been checked using PDB's structure validation
software, but annotation is limited to bibliographic citations,
primary sequence data, and other essential information. PDB
plans to complete full annotation of all structures in time for
the August 1993 Beijing International Union of Crystallography
(IUCr) Congress when a total of 2,300 entries is expected.
Current trends suggest that the number of depositions in PDB is
growing exponentially and, if this is indeed the case, a total
of more than 10,000 entries can be expected by the end of 1998.

The entire PDB collection of prerelease and full-release entries
is now available from Brookhaven free of charge over Internet.
Distribution via Internet is expected to continue to increase in
importance in the future. For details on how to access the PDB
e-mail server and anonymous FTP, see page 5. If you wish to
purchase PDB data from Brookhaven on CD ROM or magnetic tape,
please use the Brookhaven Order Form on pp. 13-14. The database
is also available from the PDB Affiliated Centers listed on page

Important new developments presently underway at PDB include the

  o  PDB has officially adopted the IUCr's Crystallographic
     Information File (CIF) standard as its future data
     interchange format. The ASN.1 interchange standard used in
     a number of molecular biology databases also will be
     supported. Support of the traditional PDB fixed
     field-length format will continue in parallel with CIF and
     ASN.1 for several years.

  o  Data entry will, as much as possible, be performed by the
     depositors. PDB will set standards for an open, extensible
     PDB-AUTHORIN data entry software system and a validation
     suite incorporating PDB and community-supplied modules. PDB
     will maintain the AUTHORIN and validation suite software
     products through regular public releases.

  o  An on-line PDB database will be developed which will
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     oriented database technology will be considered as well.

In fulfilling its goals and objectives, PDB is relying on an
extensive network of collaborations with members of the
community. These collaborations are central to all three areas
of development highlighted above and are expected to assume
greater importance in the future.

Thomas F. Koetzle
Head, PDB
January 1993 PDB Release
	1055	fully annotated atomic coordinate entries
		(53 new full-release entries)

	944	proteins, enzymes and viruses
	90	DNA's
	2	RNA's
	9	tRNA's
	10	carbohydrates

	437	prerelease atomic coordinate entries
	270	structure factor entries
	23	NMR experimental entries

The total size of the atomic coordinate entry database is 375
Mbytes, uncompressed.
Issuing Idcodes
New procedures giving depositors direct access to PDB processing
and checking programs via Internet will be available for
depositor testing starting in March 1993. Depositors using these
new procedures can expect to receive confirmation of their
deposition along with their entry idcode within three days of
deposition. Further details and login instructions will be
available shortly on the PDB anonymous FTP account.

Several options will be available to speed up the deposition

  o  Files that are in standard PDB format will be processed for
     prerelease directly with minimal staff intervention. This
     new procedure will require files to be fully annotated and
     to conform to standard PDB data representation.

  o  Depositors can enter annotation directly into PDB-SYBASE
     deposition tables using an interface developed at
     Brookhaven. Atomic coordinate data must be submitted in
     PDB format.

  o  A new PDB deposition form is being formulated. This new
     form is expected to facilitate transcription of information
     directly into PDB-SYBASE tables.
PDB Data Interchange Format
The PDB has adopted the IUCr's Crystallographic Information File
(CIF) as its future data interchange format. Based on the
Self-Defining Text Archive and Retrieval (STAR) procedure [1],
the CIF is a general free-format text archive file. A
comprehensive CIF dictionary of crystallographic data items for
reporting results emanating from structural studies of small
organic and inorganic molecules already has been adopted by the
IUCr [2]. Union journals now accept for publication manuscripts
and data written in CIF format.

A Working Group on Macromolecular CIF Definitions of the IUCr
Commission on Crystallographic Data and the IUCr Commission on
Journals, headed by Dr. P. M. D. Fitzgerald, is working at
extending the CIF dictionary to represent results from
structural studies of biological macromolecules. The Working
Group is presenting the macromolecular extensions to the core
dictionary to the IUCr for formal approval at the XVIth Congress
and General Assembly of the IUCr to be held in Beijing, China in
August 1993. The Working Group actively is seeking input from
the community concerning the macromolecular CIF dictionary. A
presentation of the dictionary will be made at the Annual
Meeting of t

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