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

• Published in: Acta crystallographica. Section B, Structural science Vol. 48 ( Pt 6); p. 790
• Main Authors: Guss, J M, Bartunik, H D, Freeman, H C
• Format: Journal Article
• Language: English
• Published: United States 01-12-1992
• Subjects: Amino Acid Sequence; Copper - chemistry; Least-Squares Analysis; Molecular Sequence Data; Molecular Structure; Plant Proteins - chemistry; Plastocyanin - chemistry; Protein Conformation; Protein Structure, Tertiary; Solvents - chemistry; X-Ray Diffraction
• ISSN: 0108-7681
• DOI: 10.1107/S0108768192004270

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(1)2(1)2(1), 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 alpha 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 anomalous-scattering corrections on the copper-site geometry have been explored. The final values of the Cu-ligand bond lengths are: Cu--N(His37) 1.91, Cu--S(Cys84) 2.07, Cu--N(His87) 2.06, Cu--S(Met92) 2.82 A.