Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 Å resolution

Abstract

The structure of the electron-transfer protein, plastocyanin (99 amino acids, one Cu atom, 10 500 Da) from poplar leaves, has been refined at 1.33 A resolution to a residual R=0.15. The space group is orthorhombic, P2~2~2~, a = 29.60 (1), b = 46.86 (3), c = 57.60 (3)A. The 14 303 reflections used in the refinement were obtained from a data set recorded on a four-circle diffractometer with radiation from a sealed fine-focus tube, combined with a data set measured on oscillation films exposed at the DESY synchrotron. The final model comprises 1442 (738 non-H) protein atoms, one Cu atom and 110 solvent molecules. Nine residues are described as disordered. The root-mean-square deviation from ideal bond lengths is 0.016 A and the root-mean-square difference between the positions of the C" atoms in this refined model and in the structure previously refined at 1.6 A resolution is 0.11 A. The effects of manual model adjustment, resolution, choice of standard values for geometrical parameters, inclusion of H atoms and inclusion of anomalousscattering corrections on the copper-site geometry have been explored. The final values of the Culigand bond lengths are: Cu--N(His37) 1.91, Cu--S(Cys84) 2.07, Cu--N(His87) 2.06, Cu--S(Met92) 2.82 A.

The 1.6 Å resolution crystal structure of a mutant plastocyanin bearing a 21–25 engineered disulfide bridge

“…The B-factor pro®les of mut-PC molecules A and B have been normalized to that of wild-type PC by assigning the same B-factor value to the respective N-terminal residues. Guss et al (1992). ³ S-(thioethylhydroxy)cystine (Kleywegt & Jones, 1998).…”

“…2). Remarkably, the 32±68 loop in wild-type PC hosts most of the negatively charged patch involved in intermolecular contacts with cytochrome f (Guss et al, 1992;Redimbo et al, 1994). Therefore, such a transition from ā exible loop structure (in the absence of intermolecular contacts) to a rigid protein structure (in the presence of crystal contacts) may re¯ect a functional property speci®cally coded in the PC structure to promote/mediate interactions with molecular partners.…”

“…The search model was the wild-type poplar PC solved at 1.33 A Ê resolution (PDB code 1plc; Guss et al, 1992), whose residues 21 and 25 had been truncated at the C atoms and the active-site Cu atom removed. The correlation coef®cient after positioning the ®rst molecule was 0.292, with an R factor of 0.566; after positioning the second molecule the correlation coef®cient was 0.534, with an R factor of 0.469.…”

“…Strikingly, the new crystal form obtained displays two mut-PC molecules per asymmetric unit. Structural perturbations induced by the engineered disul®de are discussed in light of the well characterized wild-type PC structure (Guss et al, 1992).…”

Crystal structure of spinach plastocyanin at 1.7 Å resolution

“…Here we report the first crystal structure of the spinach PC at 1.7 8, resolution, and compare it to the structure of the oxidized poplar protein at 1.33 A resolution (Guss et al, 1992).…”