Section 24.4.3. BMCD data

The BMCD contains both data extracted from the literature defining the macromolecules and data describing the crystallization and crystal form. Macromolecule data are included for biological macromolecules for which crystals have been obtained that are suitable for diffraction studies. Crystal entries must have unique unit-cell constants. Both macromolecule and crystal entries are assigned a four-character alphanumeric identifier, beginning with M or C for macromolecule and crystal, respectively.

Macromolecule data . Each macromolecule entry includes the name of the macromolecule and other aliases. Each entry includes biological source information that includes the common name, genus, species, tissue, cell and organelle from which the macromolecule was isolated. Attempts have also been made to include this information for recombinant proteins expressed in a foreign host. The subunit composition and molecular weight are also included. This information consists of the total number of subunits, the number of each type of distinct subunit, the total molecular weight and the molecular weight for each type of individual subunit. (A subunit of a biological macromolecule entity is defined as a part of the assembly that is associated with another part by non-covalent interactions. For example, haemoglobin has four subunits, two α-globins and two β-globins, and the two oligomeric nucleic acid strands of a double-stranded nucleic acid fragment are considered as two subunits.) A representative macromolecule entry is illustrated in Fig. 24.4.3.1.

Figure 24.4.3.1| top | pdf | A representative example of a biological macromolecule, subtilisin BPN′: prodomain, entry M1MT in the BMCD.

Crystallization and crystal data . The data in each crystal entry include the crystal data, crystal morphology, the experimental details of the crystallization procedure and complete references. The crystal data include the unit-cell dimensions (a, b, c, α, β, γ), the number of molecules in the unit cell (Z), the space group and the crystal density. The crystal size and shape are given along with the diffraction quality. If crystal photographs or diffraction pictures are published, the appropriate references are indicated. The experimental details include the macromolecule concentration, the temperature, the pH, the chemical additives to the growth medium, the crystallization method and the length of time required to produce crystals of a size suitable for diffraction experiments. A description of the procedure is provided if the crystallization protocol deviates from methods that are in general use. Cross-references to two other structural biology databases, the Protein Data Bank (Chapter 24.5 ) and the Nucleic Acid Database (Berman et al., 1992), are given if the identifiers are known. One of the crystal entries for the macromolecule entry illustrated in Fig. 24.4.3.1 is shown in Fig. 24.4.3.2.

Figure 24.4.3.2| top | pdf | A representative example of a crystal entry C2CK for the subtilsin BPN′: prodomain, entry M1MT in the BMCD.