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. 2011 Dec 15;27(24):3392-8.
doi: 10.1093/bioinformatics/btr590. Epub 2011 Oct 27.

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

Robbie P Joosten  1 , Krista Joosten, Serge X Cohen, Gert Vriend, Anastassis Perrakis
Affiliations

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

Robbie P Joosten et al. Bioinformatics. .

Abstract

Motivation: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users.

Results: We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods.

Availability and implementation: The PDB_REDO database and links to all software are available at http://www.cmbi.ru.nl/pdb_redo.

Contact: r.joosten@nki.nl; a.perrakis@nki.nl

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Examples of model rebuilding performed in PDB_REDO. (A) A peptide flip improves the fit with the 2mFo-DFc ED map (light blue, contoured at 1.3 r.m.s.) and removes the difference peaks in the mFo-DFc difference map (green [+] and red [−], contoured at 3.0 r.m.s.), while creating a new hydrogen bond (dotted line) (PDB:155C). (B) Rebuilding the side chain results in a better fit (PDB:1OVO). (C) The previously missing nitrogen atoms make the ionic interaction with the negatively charged C-terminus of the protein obvious (PDB:2TPI). (D) Flipping the histidine and rebuilding the threonine, results in a net gain of three hydrogen bonds (PDB:3JXV).
Fig. 2.
Fig. 2.
Box-and-whiskers plots for structure model quality metrics calculated for the original PDB entries and after PDB-REDO. The open boxes show the ‘legacy’ PDB files, the filled boxes the ‘recent’ dataset. The whiskers cover all data points within 1.5 times the inter-quartile range and the circles denote outliers. The dotted lines mark the PDB averages. (A) R-factor. (B) Ramachandran plot Z-score from WHAT_CHECK. (C) All-atom Clashscore from MolProbity as percentile relative to PDB entries of similar resolution.
Fig. 3.
Fig. 3.
Examples of peptide flips and the fit to corresponding ED maps (light blue, contoured at 1.1 r.m.s.) before and after PDB_REDO. For each flip, the change in backbone torsion angles of the two residues involved is marked by arrows in the Ramachandran plot.
Fig. 4.
Fig. 4.
Examples of side chain remodeling and the fit to corresponding ED maps (light blue, contoured at 1.3 r.m.s.) before and after PDB_REDO. The arrows in the Ramachandran plots show the change in the backbone torsion angles after rebuilding (examples from 155c).
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