3H9A

Crystal structure of BacB, an enzyme involved in Bacilysin synthesis, in triclinic form

Summary for 3H9A

• Entry DOI: 10.2210/pdb3h9a/pdb
• Related: 3h7j 3h7y
• Descriptor: Bacilysin biosynthesis protein bacB, COBALT (II) ION, 3-PHENYLPYRUVIC ACID, ... (5 entities in total)
• Functional Keywords: bacb, ywfc, bacilysin synthesis, anticapsin synthesis, bi-cupin, double stranded beta helix, antibiotic biosynthesis, biosynthetic protein
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 57732.75

Authors

Rajavel, M.,Gopal, B. (deposition date: 2009-04-30, release date: 2010-03-02, Last modification date: 2024-10-09)

Primary citation

Rajavel, M.,Gopal, B.
Analysis of multiple crystal forms of Bacillus subtilis BacB suggests a role for a metal ion as a nucleant for crystallization
Acta Crystallogr.,Sect.D, 66:635-639, 2010

PubMed Abstract: Bacillus subtilis BacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded beta-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalized B-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.

PubMed: 20445239
DOI: 10.1107/S0907444910006682

Experimental method

X-RAY DIFFRACTION (2.04 Å)