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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 24.5, pp. 675-684
https://doi.org/10.1107/97809553602060000722 Chapter 24.5. The Protein Data Bank, 1999–
H. M. Berman,a* J. Westbrook,a Z. Feng,a G. Gilliland,b T. N. Bhat,b H. Weissig,c I. N. Shindyalovc and P. E. Bourned
a
Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA,bNational Institute of Standards and Technology, Biotechnology Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA,cSan Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA, and dDepartment of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA In 1998, members of the Research Collaboratory for Structural Bioinformatics became the managers of the Protein Data Bank archive. This chapter details the systems used for the deposition, annotation and distribution of the data in the archive. Keywords: databases; nuclear magnetic resonance; NMR; Protein Data Bank; structure validation. |
The Protein Data Bank (PDB) was established at Brookhaven National Laboratory (BNL) (Bernstein et al., 1977![[link]](/graphics/greenarr.gif)
) in 1971 as an archive for biological macromolecular crystal structures. In the beginning there were seven structures, and each year a handful more were deposited. In the 1980s the number of deposited structures began to increase dramatically. This was due to the improved technology for all aspects of the crystallographic process, the addition of structures determined by nuclear magnetic resonance (NMR) methods and changes in the community views about data sharing. By the early 1990s the majority of journals required a PDB accession code and at least one funding agency (National Institute of General Medical Sciences) adopted the guidelines published by the IUCr requiring data deposition for all structures.
The mode of access to PDB data has changed over the years as a result of improved technology, notably the availability of the World Wide Web (WWW) replacing distribution solely via magnetic media. Further, the need to analyse diverse data sets required the development of modern data-management systems.
Initial use of the PDB had been limited to a small group of experts involved in structural research. Today depositors to the PDB have varying expertise in the techniques of X-ray crystal-structure determination, NMR, cryoelectron microscopy and theoretical modelling. Users are a very diverse group of researchers in biology and chemistry, community scientists, educators and students at all levels. The tremendous influx of data soon to be fuelled by the structural genomics initiative, and the increased recognition of the value of the data toward understanding biological function, demand new ways to collect, organize and distribute the data.
The vision of the Research Collaboratory for Structural Bioinformatics (RCSB)1 is to create a resource based on the most modern technology that would facilitate the use and analysis of structural data and thus create an enabling resource for biological research. In October 1998, the management of the PDB became the responsibility of the RCSB.2 In this chapter, we describe the current procedures for deposition, processing and distribution of PDB data by the RCSB. We conclude with some current developments of the PDB.
A key component of creating the public archive of information is the efficient capture and curation of the data – data processing. Data processing consists of data deposition, annotation and validation. These steps are part of the fully documented and integrated data-processing system shown in Fig. 24.5.2.1.
![[Figure 24.5.2.1]](/figures/Fafig24o5o2o1thm.gif) | The steps in PDB data processing. Ellipses represent actions and rectangles define content. |
In the present system (Fig. 24.5.2.2), data (atomic coordinates, structure factors and NMR restraints) may be submitted via e-mail or via the AutoDep Input Tool [ADIT: http://deposit.rcsb.org/adit/
(Westbrook et al., 1998)] developed by the RCSB. ADIT, which is also used to process the entries, is built on top of the mmCIF dictionary, which is an ontology of 1700 terms that define the macromolecular structure and the crystallographic experiment (Bourne et al., 1997), and a data-processing program called MAXIT (Macromolecular Exchange and Input Tool; Feng, Hsieh et al., 1998). This integrated system helps to ensure that the data that are deposited for an entry are consistent and error-free after annotation.
![[Figure 24.5.2.2]](/figures/Fafig24o5o2o2thm.gif) | The integrated tools of the PDB data-processing system. |
After a structure has been deposited using ADIT, a PDB identifier is sent to the author automatically and immediately (Fig. 24.5.2.1, step 1). This is the first stage in which information about the structure is loaded into the internal core database (see Section 24.5.3). The entry is then annotated by PDB staff using ADIT; several validation reports about the structure are produced. The completely annotated entry as it will appear in the PDB resource, together with the validation information, is sent back to the depositor (step 2). After reviewing the processed file, the author sends any revisions (step 3). Depending on the nature of these revisions, steps 2 and 3 may be repeated. Once approval is received from the author (step 4), the entry and the tables in the internal core database are ready for distribution.
All aspects of data processing, including communications with the author, are recorded and stored in the correspondence archive. This makes it possible for the PDB staff to retrieve information about any aspect of the deposition process and to monitor the efficiency of PDB operations closely.
Current status information including a list of authors, title and release category is stored for each entry in the core database and is made accessible for query via the WWW interface (http://www.rcsb.org/pdb/status.html ). Entries before release are categorized as `in processing' (PROC), `in depositor review' (WAIT), `to be held until publication' (HPUB) or `on hold until a depositor specified date' (HOLD).
All the data collected from depositors by the PDB are considered primary data. Primary data contain, in addition to the coordinates, general information required for all deposited structures and information specific to the method of structure determination. Table 24.5.2.1 contains the general information that the PDB collects for all structures as well as the additional information collected for those structures determined by X-ray methods. The additional items listed for the NMR structures are derived from the International Union of Pure and Applied Chemistry recommendations (Markley et al., 1998) and will be implemented in the near future.
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The information content of data submitted by the depositor is likely to change as new methods for data collection, structure determination and refinement evolve and advance. In addition, the ways in which these data are captured is likely to change as the software for structure determination and refinement produce the necessary data items as part of their output. The data-input system for the PDB, ADIT, has been designed so as to incorporate these likely changes easily.
Validation refers to the procedure for assessing the quality of deposited atomic models (structure validation) and for assessing how well these models fit the experimental data (experimental validation). The PDB validates structures using accepted community standards as part of ADIT's integrated data-processing system. All validation reports are communicated directly to the depositor. It is also possible to run these validation checks against structures that are not being deposited. A validation server (http://deposit.rcsb.org/validate/ ) has been made available for this purpose.
Several types of checks are used in this process: PROCHECK (Laskowski et al., 1993) is used for checking the structural features of proteins and NUCheck (Feng, Westbrook & Berman, 1998) is used for checking the structural features of nucleic acids. The information currently checked includes the following: bond lengths and bond angles, nomenclature, sequence, stereochemistry, torsion angles, ligand geometry, planarity of peptide bonds, intermolecular contacts, and positions of water molecules. In consultation with the community, other structure checks will be implemented over the next few years.
The experimental data are also checked. Currently, X-ray crystallographic data are validated and plans for checking NMR data are in progress. For X-ray crystallographic structures, the structure factors are validated using SFCHECK (Vaguine et al., 1999). This program extracts the deposited R factor, resolution and model information, and then compares them with values calculated from coordinate and structure-factor files. It also calculates an overall B factor, coordinate errors, an effective resolution and completeness. The summary of the density correlation shift and B factor are reported for each residue. As specific procedures are developed for checking NMR structures against experimental data, they will be incorporated into the PDB validation procedures.
The PDB staff recognize that NMR data need a special development effort. Historically these data have been retro-fitted into a PDB format defined around crystallographic information. As a first step towards improving this situation, the PDB carried out an extensive assessment of the current NMR holdings and presented the findings to a task force consisting of a cross section of NMR researchers. The PDB is working with this group, the BioMagResBank (BMRB; Ulrich et al., 1989) and other members of the NMR community to develop an NMR data dictionary along with deposition and validation tools specific for NMR structures.
Production processing of PDB entries by the RCSB began on 27 January 1999. As of 1 July 1999, when the RCSB became fully responsible for the PDB, approximately 80% of all structures submitted to the PDB are deposited via ADIT and processed by the RCSB. Another 20% are submitted via AutoDep to the European Bioinformatics Institute (EBI), who process these submissions and forward them to the PDB for archiving and distribution. The average time from deposition to the completion of data processing including author interactions is two weeks. The number of structures with a HOLD release status remains at about 20% of all submissions; 57% are held until publication (HPUB); and 23% are released immediately after processing.
Table 24.5.2.2 shows the breakdown of the types of structures in the PDB. As of 14 September 1999, the PDB contained 10 714 publicly accessible structures with another 1169 entries on hold (not shown). Of these, 8789 (82%) were determined by X-ray methods, 1692 (16%) were determined by NMR and 233 (2%) were theoretical models. Overall, 35% of the entries have deposited experimental data.
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In recognition of the fact that no single architecture can fully express the information content of the PDB, an integrated system of heterogeneous databases and indices that store and organize the structural data has been created. At present there are five major components (Fig. 24.5.3.1):
![[Figure 24.5.3.1]](/figures/Fafig24o5o3o1thm.gif)
In the current implementation, communication among databases has been accomplished using the common gateway interface (CGI). An integrated web interface dispatches a query to the appropriate database(s), which then executes the query. Each database returns the PDB identifiers that satisfy the query, and the CGI program integrates the results. Complex queries are performed by repeating the process and having the interface program perform the appropriate Boolean operation(s) on the collection of query results. A variety of output options are then available for use with the final list of selected structures.
The CGI approach (and in the future a CORBA-based approach) will permit other databases to be integrated into this system, for example, those containing extended data on different protein families. The same approach could also be applied to include NMR data found in the BMRB or data found in other community databases.
Three distinct query interfaces are available for querying data within the PDB: Status Query (http://www.rcsb.org/pdb/status.html
), SearchLite (http://www.rcsb.org/pdb/searchlite.html
) and SearchFields (http://www.rcsb.org/pdb/cgi/queryForm.cgi
). Table 24.5.3.1 summarizes the current query and analysis capabilities of the PDB. Fig. 24.5.3.2 illustrates how the various query options are organized.
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![[Figure 24.5.3.2]](/figures/Fafig24o5o3o2thm.gif) | The various query options that are available for the PDB. |
SearchLite
, which provides a single form field for keyword searches, was introduced in February 1999. All textual information within the PDB files as well as dates and some experimental data are accessible via simple or structured queries. SearchFields, accessible since May 1999, is a customizable query form that allows searching over many different data items, including compound, citation authors, sequence (via a FASTA search; Pearson & Lipman, 1988) and release or deposition dates.
Two user interfaces provide extensive information for results sets from SearchLite or SearchFields queries. The `Query result browser' interface allows access to some general information, access to more detailed information in tabular format and the possibility of downloading whole sets of data files for result sets consisting of multiple PDB entries. The `Structure explorer' interface provides information about individual structures as well as cross-links to many external resources for macromolecular structure data (Table 24.5.3.2). Both interfaces are accessible to other data resources through the simple CGI application programmer interface (API) described at http://www.rcsb.org/pdb/linking.html
.
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Table 24.5.3.3 indicates that usage has climbed dramatically since the system was first introduced in February 1999. Currently the PDB receives approximately 90 000 web hits per day, or, on average, one query every second, seven days a week, 24 hours a day.
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Data are distributed to the community in the following ways:
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Data available for distribution include PDB files, mmCIF files, derived information, structure factors, NMR restraints, documentation, data dictionaries and software.
The RCSB has been responsible for distribution of PDB data since 3 February 1999. Data are distributed once a week. New data officially become available at 1 a.m. Pacific Standard Time each Wednesday. This follows the tradition developed by BNL and has minimized the impact of the transition on existing mirror sites. Since May 1999, two ftp archives have been provided: ftp://ftp.rcsb.org , a reorganized and more logical organization of all PDB data, software and documentation; and ftp://bnlarchive.rcsb.org , a near-identical copy of the original BNL archive which is maintained for purposes of backward compatibility. RCSB-style PDB mirrors have been established in Japan (Osaka University), Singapore (National University Hospital), Brazil (Universidade Federal de Minas Gerais Brazil) and in the UK (the Cambridge Crystallographic Data Centre). Plans call for operating mirrors in Australia, Canada, Germany and possibly India.
The first PDB CD-ROM distribution by the RCSB contained the coordinate files, experimental data, software and documentation as found in the PDB on 30 June 1999. Data are currently distributed as compressed files using the compression utility program gzip. Refer to http://www.rcsb.org/pdb/cdrom.html for details of how to order CD-ROM sets. There is presently no charge for this service.
The PDB is establishing a central master archiving facility. The master archive plan is based on five goals: reconstruction of the current archive in the case of a major disaster; duplication of the contents of the PDB as it existed on a specific date; preservation of software, derived data, ancillary data and all other computerized and printed information; automatic archiving of all depositions and the PDB production resource; and maintenance of the PDB correspondence archive that documents all aspects of deposition. During the transition period, all physical materials including electronic media and hard-copy materials were inventoried and stored, and are being catalogued.
One of the goals of the PDB has been to provide a smooth transition from the system at BNL to the new system. Accordingly AutoDep, which was developed by BNL (Brookhaven National Laboratory, 1998) for data deposition, has been ported to the RCSB site and enables depositors to complete partial depositions as well as to make new depositions. In addition, the EBI accepts data using AutoDep. Similarly, the programs developed at BNL for data query and distribution (PDBLite, 3DB Browser etc.) are being maintained by the remaining BNL-style mirrors. The RCSB provides data in a form usable by these mirrors. Finally, the style and format of the BNL ftp archive is being maintained at ftp://bnlarchive.rcsb.org
.
Links to the PDB at BNL were automatically redirected to the RCSB after BNL closed operations on 30 June 1999 using a network redirect implemented jointly by RCSB and BNL staff. External resources linking to the PDB are advised to change any URLs from http://www.pdb.bnl.gov to http://www.rcsb.org .
An important role of the PDB is to foster new standards and technologies important to researchers and educators using macromolecular structure data. To this end, the following are under development at the PDB.
The RCSB is leading the Object Management Group Life Sciences Initiative's efforts to define a CORBA interface definition for the representation of macromolecular structure data. This is a standard developed under a strict procedure to ensure maximum input by members of various academic and industrial research communities. At this stage, proposals for the interface definition, including a working prototype that uses the standard, are being accepted. For further details refer to http://www.omg.org/cgi-bin/doc?lifesci/99–08-15 . The finalized standard interface will facilitate the query and exchange of structural information not just at the level of complete structures, but at finer levels of detail.
As multimedia become more common, the opportunity exists to use them to deliver information on structure and function to a broad PDB user community via the web. To date we have developed prototype protein documentaries (Quinn, Taylor et al., 1999) that explore these new media in describing structure–function relationships in proteins. It is also possible to develop educational materials that will run using a recent web browser (Quinn, Wang et al., 1999).
Finally, it is recognized that structures exist both in the public and private domains. To this end we are planning on providing a subset of database tools for local use. Users will be able to load both public and proprietary data and use the same search and exploratory tools used at the PDB resources.
The PDB has several advisory boards. Each member institution of the RCSB has its own local PDB Advisory Committee. Each institution is responsible for implementing the recommendations of those committees, as well as the recommendations of an international advisory board. Initially, the RCSB presented a report to the advisory board previously convened by BNL. At their recommendation, a new board has been assembled which contains previous members and new members. The goal was to have the board accurately reflect the depositor and user communities and thus include experts from many disciplines.
Serious issues of policy are referred to the major scientific societies, notably the International Union of Crystallography (IUCr). The goal is to make decisions based on input from a broad international community of experts. The IUCr maintains the mmCIF dictionary as the data standard upon which the PDB is built.
The PDB seeks to keep the community informed of new developments via weekly news updates to the web site, quarterly newsletters and an annual report. Users can request information at any time by sending an e-mail to info@rcsb.org
. Finally, the pdb-l@rcsb.org listserver provides a community forum for the discussion of PDB-related issues. Changes to PDB operations that may affect the community, for example data-format changes, are posted here and users have 60 days to discuss the issue before changes are made according to major consensus. Table 24.5.9.1 indicates how to access these resources.
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These are exciting and challenging times to be responsible for the collection, curation and distribution of macromolecular structure data. Since the RCSB assumed responsibility for data deposition in February 1999, the number of depositions has averaged approximately 50 a week. However, with the advent of a number of structure genomics initiatives worldwide, this number is likely to increase. We estimate that the PDB, which at writing contains approximately 10 500 structures, could triple or quadruple in size over the next five years. This presents a challenge of timely distribution while maintaining high quality. The PDB's approach of using modern data-management practices should permit us to accommodate a large data influx.
The maintenance and further development of the PDB are community efforts. The willingness of others to share ideas, software and data provides a depth to the resource not obtainable otherwise. Some of these efforts are acknowledged below. New input is constantly being sought and the PDB invites comments at any time by e-mail to info@rcsb.org .
Acknowledgements
The continuing support of Ken Breslauer (Rutgers), John Rumble (NIST) and Sid Karin (SDSC) is gratefully acknowledged. Current collaborators contributing to the future development of the PDB are the BioMagResBank, the Cambridge Crystallographic Data Centre, the HIV Protease Database Group, The Institute for Protein Research, Osaka University, The National Center for Biotechnology Information, the ReLiBase developers, the Swiss Institute for Bioinformatics/Glaxo and the European Bioinformatics Institute.
The cooperation of the BNL PDB staff is also gratefully acknowledged.
Parts of this chapter have appeared in Nucleic Acids Research (Berman et al., 2000) and are reproduced here with permission of Oxford University Press.
This work is supported by grants from the National Science Foundation, the Office of Biology and Environmental Research at the Department of Energy, and two units of the National Institutes of Health: the National Institute of General Medical Sciences and the National Library of Medicine.
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