Structure of Balhimycin and its Complex with Solvent Molecules

Balhimycin is a naturally occurring glycopeptide antibiotic, related to vancomycin which acts by binding nascent bacterial cell-wall peptide ending in the sequence d-Ala-d-Ala. Crystals of balhimycin are monoclinic, space group P21, a = 20.48 (10), b = 43.93 (21), c = 27.76 (14) Å, β = 100.5 (5)° with four independent antibiotic molecules, three molecules of 2-methyl-2,4-pentanediol, two citrate ions, three acetate ions and 127.5 water molecules in the asymmetric unit. With an asymmetric unit larger than those of the smallest proteins and a solvent content of about 32%, the crystals have similar diffraction properties to those of small proteins. 27 387 unique reflections were collected using synchrotron radiation. The structure was solved by a standard protein technique, the molecular-replacement method, using ureido-balhimycin as search model. The anisotropic refinement against all F2 data between 0.96 and 45 Å converged to a conventional R value of 11.27% with R1=\sum\big| |F_o|-|F_c| \big|/\sum|F_o| for the 24 623 data with I > 2σ(I) and 12.58% for all 27 387 data. The four monomers possess fairly similar conformations (r.m.s. deviation 0.7 Å). Two antibiotic molecules form a tight dimer with antiparallel hydrogen bonds between the peptide backbone as well as between the vancosamine residues and the peptide backbone. In each of the two dimers, one binding pocket is occupied by a citrate ion and the other by an acetate ion. The dimer units are linked in the crystal by hydrogen bonds to form infinite chains.