PDB Deposition Research Articles

Fifty years of Protein Data Bank in the Journal of Biochemistry.

Protein Data Bank (PDB), jointly founded in 1971 by Brookhaven National Laboratory, USA, and the Cambridge Crystallographic Data Centre, UK, is the single global archive of experimentally determined biological macromolecular structures. PDB deposition is mandatory for publication in most scientific journals, which means ‘no PDB deposition, no structural publication’. The current PDB archive contains more than 180,000 entries and includes many structures from Asian institutions. The first protein structure from Japan was that of cytochrome c determined by Prof Masao Kakudo’s group at the Institute for Protein Research, Osaka University, in 1971 at a resolution of 4 Å, and a subsequent atomic structure at 2.3 Å resolution was deposited to PDB in 1976 as the 1st Asian and 21st entry of the entire PDB archive. Since then, 317 protein structures whose primary citation was the Journal of Biochemistry (J. Biochem.) have been deposited to PDB. Based on this long history between PDB and J. Biochem., a statistical analysis of all structural reports in J. Biochem. has been carried out using the relational database system at PDBj (https://pdbj.org) and reviewed the yearly distribution, resolution, quality of structure, type of target protein, number of citations and comparison against other major journals.

IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition.

The web-based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications. It also records and tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects. Fully automated data collection is now possible at several synchrotrons, which means that the number of samples tested at the synchrotron is currently increasing rapidly. Therefore, the protein crystallography research communities at the University of Oulu, Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron. In IceBear, each crystal selected for data collection is given a unique sample name and a crystal page is generated. Subsequently, the metadata required for data collection are uploaded directly to the ISPyB synchrotron database by a shipment module, and for each sample a link to the relevant ISPyB page is stored. IceBear allows notes to be made for each sample during cryocooling treatment and during data collection, as well as in later steps of the structure determination. Protocols are also available to aid the recycling of pins, pucks and dewars when the dewar returns from the synchrotron. The IceBear database is organized around projects, and project members can easily access the crystallization and diffraction metadata for each sample, as well as any additional information that has been provided via the notes. The crystal page for each sample connects the crystallization, diffraction and structural information by providing links to the IceBear drop-viewer page and to the ISPyB data-collection page, as well as to the structure deposited in the Protein Data Bank.

Local and global analysis of macromolecular atomic displacement parameters.

This paper describes the global and local analysis of atomic displacement parameters (ADPs) of macromolecules in X-ray crystallography. The distribution of ADPs is shown to follow the shifted inverse-gamma distribution or a mixture of these distributions. The mixture parameters are estimated using the expectation-maximization algorithm. In addition, a method for the resolution- and individual ADP-dependent local analysis of neighbouring atoms has been designed. This method facilitates the detection of mismodelled atoms, heavy-metal atoms and disordered and/or incorrectly modelled ligands. Both global and local analyses can be used to detect errors in atomic models, thus helping in the (re)building, refinement and validation of macromolecular structures. This method can also serve as an additional validation tool during PDB deposition.

ValTrendsDB: bringing Protein Data Bank validation information closer to the user.

SummaryStructures in PDB tend to contain errors. This is a very serious issue for authors that rely on such potentially problematic data. The community of structural biologists develops validation methods as countermeasures, which are also included in the PDB deposition system. But how are these validation efforts influencing the structure quality of subsequently published data? Which quality aspects are improving, and which remain problematic? We developed ValTrendsDB, a database that provides the results of an extensive exploratory analysis of relationships between quality criteria, size and metadata of biomacromolecules. Key input data are sourced from PDB. The discovered trends are presented via precomputed information-rich plots. ValTrendsDB also supports the visualization of a set of user-defined structures on top of general quality trends. Therefore, ValTrendsDB enables users to see the quality of structures published by selected author, laboratory or journal, discover quality outliers, etc. ValTrendsDB is updated weekly.Availability and implementationFreely accessible at http://ncbr.muni.cz/ValTrendsDB. The web interface was implemented in JavaScript. The database was implemented in C++.Supplementary information Supplementary data are available at Bioinformatics online.

Making glycoproteins a little bit sweeter with PDB-REDO.

Glycosylation is one of the most common forms of protein post-translational modification, but is also the most complex. Dealing with glycoproteins in structure model building, refinement, validation and PDB deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools. Also, experimentalists are typically less experienced in dealing with carbohydrate residues than with amino-acid residues. The results of the reannotation and re-refinement by PDB-REDO of 8114 glycoprotein structure models from the Protein Data Bank are analyzed. The positive aspects of 3620 reannotations and subsequent refinement, as well as the remaining challenges to obtaining consistently high-quality carbohydrate models, are discussed.

Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)

Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)

Re-refinement of 4xan: hen egg-white lysozyme with carboplatin in sodium bromide solution

A re-refinement of 4xan, hen egg-white lysozyme (HEWL) with carboplatin crystallized in NaBr solution, has been made and is published here as an addendum to Tanley et al. [(2014), Acta Cryst. F70, 1135-1142]. This follows a previous re-refinement and PDB deposition (4yem) by Shabalin et al. [(2015), Acta Cryst. D71, 1965-1979]. The critical evaluation of the original PDB deposition (4xan), and the subsequent critical examination of the re-refined structure (4yem), has led to an improved model (PDB code 5hmj).

Correction to ‘The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold’

Open AccessMoreSectionsView PDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmail Cite this article Schulte Tim, Löfling Jonas, Mikaelsson Cecilia, Kikhney Alexey, Hentrich Karina, Diamante Aurora, Ebel Christine, Normark Staffan, Svergun Dmitri, Henriques-Normark Birgitta and Achour Adnane 2014Correction to ‘The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold’Open Biol.4140172140172http://doi.org/10.1098/rsob.140172SectionOpen AccessCorrectionCorrection to ‘The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold’ Tim Schulte Tim Schulte Google Scholar Find this author on PubMed Search for more papers by this author , Jonas Löfling Jonas Löfling Google Scholar Find this author on PubMed Search for more papers by this author , Cecilia Mikaelsson Cecilia Mikaelsson Google Scholar Find this author on PubMed Search for more papers by this author , Alexey Kikhney Alexey Kikhney Google Scholar Find this author on PubMed Search for more papers by this author , Karina Hentrich Karina Hentrich Google Scholar Find this author on PubMed Search for more papers by this author , Aurora Diamante Aurora Diamante Google Scholar Find this author on PubMed Search for more papers by this author , Christine Ebel Christine Ebel Google Scholar Find this author on PubMed Search for more papers by this author , Staffan Normark Staffan Normark Google Scholar Find this author on PubMed Search for more papers by this author , Dmitri Svergun Dmitri Svergun Google Scholar Find this author on PubMed Search for more papers by this author , Birgitta Henriques-Normark Birgitta Henriques-Normark Google Scholar Find this author on PubMed Search for more papers by this author and Adnane Achour Adnane Achour Google Scholar Find this author on PubMed Search for more papers by this author Tim Schulte Tim Schulte Google Scholar Find this author on PubMed Search for more papers by this author , Jonas Löfling Jonas Löfling Google Scholar Find this author on PubMed Search for more papers by this author , Cecilia Mikaelsson Cecilia Mikaelsson Google Scholar Find this author on PubMed Search for more papers by this author , Alexey Kikhney Alexey Kikhney Google Scholar Find this author on PubMed Search for more papers by this author , Karina Hentrich Karina Hentrich Google Scholar Find this author on PubMed Search for more papers by this author , Aurora Diamante Aurora Diamante Google Scholar Find this author on PubMed Search for more papers by this author , Christine Ebel Christine Ebel Google Scholar Find this author on PubMed Search for more papers by this author , Staffan Normark Staffan Normark Google Scholar Find this author on PubMed Search for more papers by this author , Dmitri Svergun Dmitri Svergun Google Scholar Find this author on PubMed Search for more papers by this author , Birgitta Henriques-Normark Birgitta Henriques-Normark Google Scholar Find this author on PubMed Search for more papers by this author and Adnane Achour Adnane Achour Google Scholar Find this author on PubMed Search for more papers by this author Published:01 October 2014https://doi.org/10.1098/rsob.140172This article corrects the followingResearch ArticleThe basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM foldhttps://doi.org/10.1098/rsob.130090 Tim Schulte, Jonas Löfling, Cecilia Mikaelsson, Alexey Kikhney, Karina Hentrich, Aurora Diamante, Christine Ebel, Staffan Normark, Dmitri Svergun, Birgitta Henriques-Normark and Adnane Achour volume 4issue 1journalTitle Open Biology01 January 2014Open Biol. 4 (Published online 15 January 2014) (doi:10.1098/rsob.130090)The residue numbers in the associated PDB files 3ZGH and 3ZGI were corrected during the PDB deposition process to have the same numbers as given in the associated Uniprot entry Q97P71. Unfortunately, we missed to update the residue numbers in the figures and text of the manuscript. The numbers in the manuscript should have an offset of −1. However, the first and last residue numbers given for the protein constructs BR187–385 and STII-BR187–385 remain valid. Previous Article FiguresRelatedReferencesDetailsRelated articlesThe basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold01 January 2014Open Biology This IssueOctober 2014Volume 4Issue 10 Article InformationDOI:https://doi.org/10.1098/rsob.140172Published by:Royal SocietyOnline ISSN:2046-2441History: Published online01/10/2014 License:© 2014 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. Citations and impact PDF Download

When good ligands go bad

"Tools for validating structural models of proteins are relatively mature and widely implemented. New protein crystallographers are introduced early on to the importance of monitoring conformance with expected φ/ψ values, favored rotamers, and local stereochemistry. The protein model is validated by the PDB at the time of deposition using criteria that are also available in the standard software packages used to refine the model being deposited. By contrast, crystallographers are typically much less familiar with procedures to validate key non-protein components of the model – cofactors, substrates, inhibitors, etc. It has been estimated that as many as a third of all ligands in the PDB exhibit preventable errors of some sort, ranging from minor deviations in expected bond angles to wholly implausible placement in the binding pocket. Following recommendations from the wwPDB Validation Task Force, the PDB recently began validating ligand geometry as an integral part of deposition processing. This means that many crystallographers will soon receive for the first time a ""grade"" on the quality of ligands in the structure they have just deposited. Some will be surprised, as I was following my first PDB deposition of 2014, at how easily bad ligand geometry can slip through the cracks in supposedly robust structure refinement protocols that their lab has used for many years. I will illustrate use of current tools for generating ligand restraints to guide model refinement. One is the jligand+coot+cprodrg pipeline integrated into the CCP4 suite. Another is the Grade web server provided as a community resource by Global Phasing Ltd. Furthermore I will show examples from recent in-house refinements of how things can still go wrong even if you do use these tools, and how we recovered. The new PDB deposition checks may expose errors in your ligand descriptions after the fact. This presentation may help you avoid introducing those errors in the first place."

Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining.

Whereas the vast majority of the more than 85 000 crystal structures of macromolecules currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of imperfections. Although this fact has been pointed out in the past, it is still worth periodic updates so that the metadata obtained by global analysis of the available crystal structures, as well as the utilization of the individual structures for tasks such as drug design, should be based on only the most reliable data. Here, selected abnormal deposited structures have been analysed based on the Bayesian reasoning that the correctness of a model must be judged against both the primary evidence as well as prior knowledge. These structures, as well as information gained from the corresponding publications (if available), have emphasized some of the most prevalent types of common problems. The errors are often perfect illustrations of the nature of human cognition, which is frequently influenced by preconceptions that may lead to fanciful results in the absence of proper validation. Common errors can be traced to negligence and a lack of rigorous verification of the models against electron density, creation of non-parsimonious models, generation of improbable numbers, application of incorrect symmetry, illogical presentation of the results, or violation of the rules of chemistry and physics. Paying more attention to such problems, not only in the final validation stages but during the structure-determination process as well, is necessary not only in order to maintain the highest possible quality of the structural repositories and databases but most of all to provide a solid basis for subsequent studies, including large-scale data-mining projects. For many scientists PDB deposition is a rather infrequent event, so the need for proper training and supervision is emphasized, as well as the need for constant alertness of reason and critical judgment as absolutely necessary safeguarding measures against such problems. Ways of identifying more problematic structures are suggested so that their users may be properly alerted to their possible shortcomings.

Big changes are ahead – a new format for crystallization communications inActa Cryst. F

The coming year 2014 will be an important year for crystallography as the scientific community throughout the world celebrates the International Year of Crystallography. Acta Cryst. F will commemorate this special event with a series of articles defining the current state-of-the-art in macromolecular crystallization, with one article appearing per month throughout 2014 and into 2015. We expect this series to be a useful resource for our readership and the wider structural biology community alike. Stay tuned. We have also been working diligently over the past two or three years to finalize new requirements and a new format for our regular articles. Maybe some of you have attended the presentations given by us at various meetings or workshops about the publication tool publBio (http://publbio.iucr.org). publBio is designed to make the preparation and submission of an article much more simple and straightforward than ever before, be it a structural or a crystallization communication. The latest version not only guides authors through the requirements for each article type but also provides a means of submitting the article directly to Acta Cryst. F, thus simplifying the first stages of the submission process. The IUCr Word template now also has some of the functionality of publBio and, just like publBio, offers the option of utilizing data from an existing PDB deposition or an mmCIF file when creating the tables in your article. In July this year, we published a contribution by Janet Newman and colleagues entitled Crystallization reports are the backbone of Acta F, but do they have any spine? (Newman et al., 2013 ▶; Weiss & Einspahr, 2013 ▶). The central message of this paper was that the information content of crystallization communications published in Acta Cryst. F varies widely. While this may not seem troubling at first glance, the notion that as many as 60% of these articles lack some essential information sparked some concern. With publBio, we have a tool that will allow us to address this issue efficiently and effectively, and that will also make a major contribution to correcting the problem. We feel that the time has come to take advantage of this by making publBio (or its counterpart in the IUCr Word template) mandatory for writing and submitting crystallization communications from 1 January 2014. We expect that you will enjoy working with publBio and we are looking forward to working with you to refine and improve it. From our perspective, another major advance is that publBio will make clear exactly what data are needed for an acceptable crystallization communication. There will of course be situations in which certain data items may not be necessary or may be unavailable, but these ‘exceptions to the rules’ are exactly those about which authors need to confer with Co-editors. Therefore, we ask our authors to make full use of publBio to ease the burden of creating their publications. Finally, we thank our authors for their continued support of our journal and wish you all Season’s Greetings and Happy Holidays. We look forward to 2014 with anticipation of all the new things this New Year will bring.

The future of crystallization communications inActa Cryst. F

This issue of Acta Cryst. F features a contribution by Janet Newman and colleagues, Crystallization reports are the backbone of Acta Cryst. F, but do they have any spine? (Newman et al., 2013 ▶). In an impressive effort, the authors examined all 264 crystallization communications (CCs) published in Acta Cryst. F during the year 2012. A central objective was to assess whether the CCs contained enough information for a skilled researcher to have a reasonable chance of reproducing the experiments described. As judged by the authors, 60% of the CCs in 2012 do not contain all the necessary information. While we have long been aware that heterogeneity in writing, editing, reviewing and revising a CC inevitably leads to different levels of information content from article to article, 60% is an alarming number indeed. In order to remedy this situation, efforts to streamline CCs have been under way for some time (Einspahr & Weiss, 2008 ▶). The initial focus of the streamlining project was on the collection of mandatory and recommended items to be included in an article. More recently these efforts have led to the development of publBio which is a new tool for the publication of CCs and other articles (http://publbio.iucr.org). While there may be some differences between our and the authors’ appraisals of what data are missing in these articles, we assert that, if all authors of CCs were to use publBio for preparing their articles, the problems described above would largely be solved. We are currently discussing whether to make the use of publBio mandatory for CCs in the near future. Other issues discussed in the Newman et al. (2013 ▶) article include the geographic distribution of CCs, the citations that CCs get, and the overwhelmingly large number of PDB depositions that have no associated CC (8321 PDB depositions in 2012 versus 264 CCs in 2012). While we do not have solutions to the potential problems arising from these issues, we do need to keep a close eye on these developments. Yet another surprising issue for us is presented in Table 2 of Newman et al. (2013 ▶). Only 74 of the 264 CCs published in 2012 have a corresponding PDB deposition. While we had assumed that most CCs published in Acta Cryst. F are cited at least once, namely when the associated structure is published, this assumption is obviously far from the case, and is undoubtedly a major reason why the impact factor of Acta Cryst. F continues to be less than one. It is not clear why so few CCs lead to deposited structures. It could be that the projects described in the CCs are discontinued or that the structure is only published many years later. Whatever the true reason, we feel a corrective measure may be needed here as well. One suggestion would be to require that structure-factor amplitudes are deposited along with publication of a CC. These data could then be made public a number of years (three years, for example) after the publication of the CC, a practice which is well established in other fields of science, such as astronomy. In summary, we expect that CCs will remain central to our journal in the years to come. At the same time we are aware of potential problems associated with CCs and we will do our best to make the content of our journal as useful to the community as possible. It goes without saying that we welcome any effort by others in that direction and we would also like to invite everybody to contribute to this ongoing process.

A label-free microRNA biosensor based on DNAzyme-catalyzed and microRNA-guided formation of a thin insulating polymer film

Herein we report a label-free microRNA (miRNA) biosensor in which the formation of a thin insulating film is used to amplify the analytical signal. Briefly, the biosensor is made of an oligonucleotide-coated gold electrode. After hybridizing with a target miRNA, free capture probe (CP) strands on the biosensor are removed by a nuclease digestion. A second hybridization with an oligonucleotide-tailed DNAzyme is performed to introduce the DNAzyme to the biosensor. The DNAzyme triggers the polymerization of 3,3′-dimethoxybenzidine (DB) in the presence of H2O2 and the hybridized miRNA-CP duplexes serve as templates to guide the deposition of poly (3,3′-dimethoxybenzidine) (PDB). The formation of the insulating PDB film alters the impedance of the biosensor, rendering it readily distinguishable by electrochemical impedance measurements. The accumulative nature of the PDB deposition drastically improves the detectability of the biosensor. A proof-of-concept study is conducted on the detection of miRNAs in total RNA extracted from cultured cells.

A Label-Free Biosensor for Electrochemical Detection of Femtomolar MicroRNAs

A simple and ultrasensitive label-free microRNA (miRNA) biosensor, based on hybridized miRNA-templated deposition of an insulating polymer film and electrochemical impedance spectroscopic detection, is described in this report. The biosensor is made of a monolayer of charge-neutral morpholino capture probes on an indium tin oxide (ITO)-coated glass slide. Upon hybridization, the neutral surface of the biosensor is converted to anionic by the hybridized miRNA strands. The deposition of the insulating polymer film, poly(3,3'-dimethoxybenzidine) (PDB), is then carried out by the horseradish peroxidase-catalyzed polymerization of 3,3'-dimethoxybenzidine in the presence of H(2)O(2). The cumulative nature of the PDB deposition process significantly enhances the sensitivity of the biosensor. Under optimized conditions, miRNA expression profiling can be performed label-freely from 5.0 fM to 2.0 pM with a detection limit of 2.0 fM. The biosensor is applied to the detection of circulating miRNAs in blood and miRNAs in total RNA extracted from cultured cells.