Missing strings of residues in protein crystal structures.

Area of Science:

• Structural biology
• Biochemistry
• Crystallography

Background:

• A significant portion of protein crystal structures in the Protein Data Bank (PDB) are incomplete, with unassigned residue positions.
• This incompleteness can introduce bias in the interpretation and application of structural data by molecular biologists.
• Understanding patterns in missing structural data is crucial for accurate protein analysis.

Purpose of the Study:

• To investigate the characteristics of missing residue segments in protein crystal structures.
• To identify residue types and properties that are prevalent in or avoid these unassigned regions.
• To provide insights for crystallographers dealing with uninterpretable electron density and for structure data users.

Main Methods:

• Analysis of a large dataset of protein crystal structures from the Protein Data Bank.
• Statistical examination of residue composition within missing segments.
• Correlation of missing regions with residue flexibility indicators such as B-factors, solvent exposure, and secondary structure.

Main Results:

• The majority of protein crystal structures contain missing strings of residues.
• Polar residues and glycine are disproportionately found within these missing segments.
• Apolar and aromatic residues are generally absent from missing regions.
• Residues flanking the missing strings exhibit characteristics of high flexibility, including high B-factors and solvent exposure.

Conclusions:

• Missing residue segments in protein crystal structures exhibit distinct compositional biases.
• Flexible residues tend to flank these unassigned regions, suggesting a link to disorder or crystallographic challenges.
• These findings offer valuable guidance for crystallographers interpreting electron density maps and for end-users of protein structural data.