Type II dehydroquinase: molecular replacement with many copies.

Area of Science:

• Structural biology
• Crystallography
• Protein science

Background:

• Type II dehydroquinase is a 150-amino-acid protein that forms dodecamers with cubic symmetry in solution.
• Crystallization can lead to various crystal forms, including those with coincident biological and crystallographic symmetry, or those with significant noncrystallographic symmetry in low-symmetry systems.
• These diverse crystal forms complicate structure determination using molecular replacement.

Purpose of the Study:

• To describe structure solutions for Type II dehydroquinase using molecular replacement, focusing on challenging crystal forms.
• To assess the performance of commonly used molecular replacement software packages.
• To analyze an unusual triclinic crystal form and elucidate its true crystallographic nature.

Main Methods:

• Molecular replacement techniques were employed for structure solution.
• Four different molecular replacement software packages were evaluated.
• Crystallographic analysis, including refinement and symmetry analysis, was performed on a specific triclinic crystal form.

Main Results:

• Structure solutions were obtained for three distinct crystal forms of Type II dehydroquinase.
• Performance of molecular replacement packages varied significantly depending on crystal symmetry and complexity.
• An unusual triclinic crystal form containing 16 dodecamers was analyzed and reclassified as an F-centered cubic crystal with frustrated symmetry, not a superlattice structure.

Conclusions:

• Molecular replacement strategies must be adapted to the specific crystallographic challenges posed by different protein crystal forms.
• The choice of molecular replacement software can critically impact the success of structure solution.
• The detailed analysis of the triclinic crystal form provides new insights into protein crystallization and symmetry in crystallography.