About Asymmetric unit and Biological unit

Introduction

The atomic coordinate data in PDB is "asymmetric unit", which includes minimum essential. It doesn't always mean actual functional unit in organisms. The functional structures are called "biological unit", some of them are equal to the asymmetric units and others are generated by the transform such as rotation, and translation.

For details about asymmetric unit and biological unit, see also Introduction to Biological Assemblies and the PDB Archive.

About Asymmetric Unit

"Asymmetric Unit" is used in either meaning of Crystal asymmetric unit or Non-Crystallographic asymmetric unit.

Crystal Asymmetric Unit

The crystal asymmetric unit is the smallest portion of a crystal structure to which symmetry operations can be applied in order to generate the complete unit cell (the crystal repeating unit). Structures analyzed by crystallographic methods are deposited in this structural unit. A crystal asymmetric unit is not always identical to the biological assembly and may in fact contain a portion of a biological assembly or multiple biological assemblies.

Non-crystallographic Asymmetric Unit

When a biomolecule is assumed to have a complete symmetry in its own structure, e.g. a virus's capsid, it is recommended to deposit the structure in the smallest unit (i.e. non-crystallographic asymmetric unit) to the PDB. To reconstruct the biological assembly, non-crystallographic symmetry operations should be applied to the deposited coordinates. Typical examples are a spherical virus with icosahedral symmetry or a rod-shaped virus with helical symmetry. 　

An image of an asymmetric unit is shown for deposited coordinates of an entry. For split entries, a complete asymmetric unit is obtained by combining each asymmetric unit. 　

About Biological Unit

The biological assembly (also sometimes referred to as the biological unit) is the macromolecular assembly that has either been shown to be or is believed to be the functional form of the molecule.

Atomic coordinates data for biological units

The coordinates are available in the PDB archive at following site:

ftp://ftp.pdbj.org/pub/pdb/data/biounit/
(PDB format is available for regular entries. Currently, PDBx/mmCIF format is available only for large entries.)

Each structural data is provided in the format described below:

non-large structures which don't excess the PDB format limitation

PDB format (as in the past for a while)

large structures which excess the PDB format limitation

PDBx/mmCIF format