Abstract
The power of X-ray crystal structure analysis as a technique is to 'see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this 'seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.
Highlights
The intricate three-dimensional structures of biomolecules describe their functionalities, which can be determined accurately by the power of X-ray crystallography
Thereby, the presentation of protein crystal structures needs to routinely include their atomic precision, which we detail over all current Protein Data Bank (PDB; Berman et al, 2000; http://www.rcsb.org) entries; we offer a user knowledge base with structural biology examples
Salt Bridges in Protein Structures (SBPS) is a knowledge base created to provide information pertaining to the ion pairs present in all the three-dimensional protein structures available in the PDB archive
Summary
The intricate three-dimensional structures of biomolecules describe their functionalities, which can be determined accurately by the power of X-ray crystallography. The diffraction precision index (DPI; Cruickshank, 1999; Blow, 2002), derived from experimental crystallographic parameters, is available for use to estimate the experimental precision of the atomic coordinates in a protein structure over a much wider range of diffraction resolutions and in effect for all cases. Thereby, the presentation of protein crystal structures needs to routinely include their atomic precision, which we detail over all current Protein Data Bank (PDB; Berman et al, 2000; http://www.rcsb.org) entries; we offer a user knowledge base with structural biology examples
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