1PLC

ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF POPLAR PLASTOCYANIN AT 1.33 ANGSTROMS RESOLUTION

Replaces:  1PCY

Summary for 1PLC

• Entry DOI: 10.2210/pdb1plc/pdb
• Descriptor: PLASTOCYANIN, COPPER (II) ION (3 entities in total)
• Functional Keywords: electron transport
• Biological source: Populus nigra
• Cellular location: Plastid, chloroplast thylakoid membrane {ECO:0000269|PubMed:1492962, ECO:0000269|PubMed:22883960, ECO:0000269|PubMed:6620385, ECO:0000269|PubMed:6698995, ECO:0000269|Ref: P00299
• Total number of polymer chains: 1
• Total formula weight: 10557.15

Authors

Guss, J.M.,Freeman, H.C. (deposition date: 1992-03-11, release date: 1993-10-31, Last modification date: 2024-02-14)

Primary citation

Guss, J.M.,Bartunik, H.D.,Freeman, H.C.
Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 A resolution.
Acta Crystallogr.,Sect.B, 48:790-811, 1992

PubMed 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(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.

PubMed: 1492962
DOI: 10.1107/S0108768192004270

Experimental method

X-RAY DIFFRACTION (1.33 Å)