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

Transforming growth factor-beta is a multifunctional cell-growth regul ator and is a member of the TGF-beta superfamily of cytokines. Each mo nomer is 112 amino acids long and the mature active form is a 25 kDa h omodimer. Recently, the crystal structure of TGF-beta 2 has been deter mined independently in two laboratories [Daopin, Piez, Ogawa and Davie s (1992). Science, 257, 369-373; Schlunegger and Grutter (1992). Natur e (London), 358, 430-434] and subsequently refined to higher resolutio ns [Daopin, Li and Davies (1993). Proteins Struct. Funct. Genet. In th e press; Schlunegger and Grutter (1993). J. Mel. Biol. In the press]. A detailed structural comparison shows that the two structures are nea rly identical with the differences mostly located on the mobile region s of the molecule. The r.m.s. differences between the two structures a re 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 facto rs 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 model ing new waters. The structural identity is striking because in one cas e 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 wit h Cruickshank's equations and 0.25 Angstrom using the empirical method of Ferry and Stroud. These estimates are comparable to the r.m.s. str ucture 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 e rror, a new application of the Cruickshank formula is presented here t o estimate the local errors. (C) 1994 International Union of Crystallo graphy