Crystallization of histone deacetylase 2

1. A composition comprising a protein in crystalline form wherein the protein consists of SEQ ID NO: 5, wherein said protein is in complex with trichostatin A and wherein the protein crystal has a crystal lattice in a P2 1 2 1 2 1 space group and unit cell dimensions, +/−5%, of a=92.1 Å, b=97.6 Å, c=138.9 Å, and α=β=γ=90°.

2. The composition according to claim 1 wherein the asymmetric unit of the crystal comprises three molecules of the protein.

3. The composition according to claim 1 wherein the protein crystal diffracts X-rays for a determination of structure coordinates to a resolution of a value equal to or less than 3.0 Angstroms.

4. A method for forming a protein crystal comprising:

forming a crystallization volume comprising a precipitant solution and a protein that consists of SEQ ID NO:5, wherein said protein is in complex with trichostatin A; and

storing the crystallization volume under conditions suitable for crystal formation of the protein; and

forming a protein crystal, wherein the protein crystal has a crystal lattice in a P2 1 2 1 2 1 space group and unit cell dimensions, +/−5%, of a=92.1 Å, b=97.6 Å, c=138.9 Å, and α=β=γ=90°.

5. The method according to claim 4 , wherein the asymmetric unit of the crystal comprises three molecules of the protein.

6. The method according to claim 4 , wherein the protein crystal diffracts X-rays for a determination of structure coordinates to a resolution of a value equal to or less than 3.0 Angstroms.

7. A method for solving the structure of the protein of SEQ ID NO:5, the method comprising:

diffracting the protein crystal of claim 1 with X-rays to produce a diffraction pattern; and

solving the structure of the protein from the diffraction pattern, thereby solving the structure of the protein of SEQ ID NO:5.

8. A method of rational drug design, the method comprising:

diffracting the protein crystal of claim 1 with X-rays to produce a diffraction pattern;

solving the structure of the protein from the diffraction pattern, thereby solving the structure of the protein of SEQ ID NO:5;

performing rational drug design using the solved structure;

identifying one or more entities that potentially associates with the protein; and

selecting the one or more entities based on the rational drug design.

9. The method according to claim 8 , the method further comprising measuring an activity of the protein when contacted with the one or more entities.

10. The method according to claim 8 , the method further comprising:

comparing activity of the protein in the presence of and in the absence of the one or more entities; and

selecting entities where activity of the protein changes depending on whether or not a particular entity is present.

11. The method according to claim 8 , the method further comprising contacting cells expressing the protein with the one or more entities and detecting a change in a phenotype of the cells when a particular entity is present.