ABSTRACT
A database application has been developed for the collection of crystallographic information. This database (the BDP) has been populated with the information found in the Protein Data Bank (PDB). The tool has been used to store crystallization data parsed out of the PDB and these data may be used to extend the crystallization information found in the Biological Macromolecule Crystallization Database (BMCD) and could be used to refine crystallization methodology. A standard is proposed for describing a crystallization experiment that will ease future crystallization data collations and analyses.
Subject(s)
Crystallization/methods , Database Management Systems , Databases, Protein , Ammonium Sulfate , Crystallography, X-Ray , Databases, Factual/standards , Databases, Protein/standards , Polyethylene Glycols , Terminology as TopicABSTRACT
Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella, resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group transfer from glutamic acid to the 4"-position of a UDP-linked ketopyranose molecule to form UDP-4-amino-4-deoxy-L-arabinose represents a key step in the lipid A modification pathway. Structural and functional studies of the ArnB aminotransferase were undertaken by combining X-ray crystallography with biochemical analyses. High-resolution crystal structures were solved for two native forms and one covalently inhibited form of S. typhimurium ArnB. These structures permitted identification of key residues involved in substrate binding and catalysis, including a rarely observed nonprolyl cis peptide bond in the active site.
