COMPARISON OF 2 CRYSTAL-STRUCTURES OF TGF-BETA-2 - THE ACCURACY OF REFINED PROTEIN STRUCTURES

Transforming growth factor-beta is a multifunctional cell-growth regulator and is a member of the TGF-beta superfamily of cytokines. Each monomer is 112 amino acids long and the mature active form is a 25 kDa homodimer. Recently, the crystal structure of TGF-beta 2 has been determined independently in two laboratories [Daopin, Piez, Ogawa and Davies (1992). Science, 257, 369-373; Schlunegger and Grutter (1992). Nature (London), 358, 430-434] and subsequently refined to higher resolutions [Daopin, Li and Davies (1993). Proteins Struct. Funct. Genet. In the press; Schlunegger and Grutter (1993). J. Mel. Biol. In the press]. A detailed structural comparison shows that the two structures are nearly identical with the differences mostly located on the mobile regions of the molecule. The r.m.s. differences between the two structures are 0.10 Angstrom for 104 pairs of C-alpha atoms, 0.15 Angstrom for 434 pairs of main-chain atoms, 0.33 Angstrom for 860 out of 890 pairs of protein atoms and a correlation of 90% between the temperature B factors of all protein atoms. Based on a comparison of the water molecules, a B value of 60.0 Angstrom(2) is recommended as the cut off for modeling new waters. The structural identity is striking because in one case the material was expressed in vivo in CHO cells whereas in the other case it was expressed in E. coli and had to be refolded in vitro. The overall coordinate errors are estimated to be 0.21 Angstrom from the Luzzati plot, 0.18 Angstrom from the sigma (A) plot, 0.24 Angstrom with Cruickshank's equations and 0.25 Angstrom using the empirical method of Ferry and Stroud. These estimates are comparable to the r.m.s. structure superposition. The r.m.s. differences correlate very well with the crystallographic B values and the relation is best described with the Cruickshank formula. In addition to the estimation of an overall error, a new application of the Cruickshank formula is presented here to estimate the local errors. (C) 1994 International Union of Crystallography