We need to do some symmetry operations on the asymmetric unit. An asymmetric unit is the smallest unique set of atomic coordinates needed to describe the repeating unit of a crystal. If we have a heterodimer (two different protein chains forming a functional complex), the asymmetric unit will typically include both chains, as it is the minimal repeating unit that represents the unique content of the crystal.
BIOMT Records: The PDB file might include REMARK 350 records, which specify rotation and translation matrices (the BIOMT matrices) to generate biological assemblies from the asymmetric unit. These matrices can be applied to the atomic coordinates to generate each symmetrical copy, and the combined coordinates represent the full assembly.
Software Tools and Databases:
PISA (Proteins, Interfaces, Structures, and Assemblies): This tool from the European Bioinformatics Institute (EBI) analyzes protein interfaces and predicts stable biological assemblies by assessing thermodynamic stability. PISA is widely used to infer the likely assembly from PDB structures when BIOMT matrices are unavailable or need validation.
EPPIC (Evolutionary Protein-Protein Interface Classifier): EPPIC can help predict biological assemblies based on evolutionary conservation of interfaces and is helpful if the assembly is not explicitly provided.
Symmetry and Space Group Information: If BIOMT matrices are not available, symmetry operations derived from the crystallographic space group may suggest possible assemblies. Software tools like PyMOL, Chimera, and Phenix can generate assemblies based on space group symmetries and visual inspection.
alex-hh
commented
1 week ago
We need to do some symmetry operations on the asymmetric unit. An asymmetric unit is the smallest unique set of atomic coordinates needed to describe the repeating unit of a crystal. If we have a heterodimer (two different protein chains forming a functional complex), the asymmetric unit will typically include both chains, as it is the minimal repeating unit that represents the unique content of the crystal.
BIOMT Records: The PDB file might include REMARK 350 records, which specify rotation and translation matrices (the BIOMT matrices) to generate biological assemblies from the asymmetric unit. These matrices can be applied to the atomic coordinates to generate each symmetrical copy, and the combined coordinates represent the full assembly.
Software Tools and Databases:
PISA (Proteins, Interfaces, Structures, and Assemblies): This tool from the European Bioinformatics Institute (EBI) analyzes protein interfaces and predicts stable biological assemblies by assessing thermodynamic stability. PISA is widely used to infer the likely assembly from PDB structures when BIOMT matrices are unavailable or need validation. EPPIC (Evolutionary Protein-Protein Interface Classifier): EPPIC can help predict biological assemblies based on evolutionary conservation of interfaces and is helpful if the assembly is not explicitly provided. Symmetry and Space Group Information: If BIOMT matrices are not available, symmetry operations derived from the crystallographic space group may suggest possible assemblies. Software tools like PyMOL, Chimera, and Phenix can generate assemblies based on space group symmetries and visual inspection.