1SDY

STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE

Summary for 1SDY

• Entry DOI: 10.2210/pdb1sdy/pdb
• Descriptor: COPPER,ZINC SUPEROXIDE DISMUTASE, COPPER (II) ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: oxidoreductase(superoxide acceptor)
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Cellular location: Cytoplasm : P00445
• Total number of polymer chains: 4
• Total formula weight: 63489.38

Authors

Djinovic, K.,Gatti, G.,Coda, A.,Antolini, L.,Pelosi, G.,Desideri, A.,Falconi, M.,Marmocchi, F.,Rotilio, G.,Bolognesi, M. (deposition date: 1991-06-14, release date: 1994-01-31, Last modification date: 2024-11-13)

Primary citation

Djinovic, K.,Gatti, G.,Coda, A.,Antolini, L.,Pelosi, G.,Desideri, A.,Falconi, M.,Marmocchi, F.,Rolilio, G.,Bolognesi, M.
Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase.
Acta Crystallogr.,Sect.B, 47:918-927, 1991

PubMed Abstract: Cu,Zn yeast superoxide dismutase was crystallized from polyethylene glycol solutions. The crystals belong to the P2(1)2(1)2 space group, with cell dimensions a = 105.3, b = 143.0, c = 62.1 A; two dimers of Mr = 32,000 each are contained in the asymmetric unit. Diffraction data at 2.5 A resolution were collected with the image-plate system at the EMBL synchrotron radiation facility in Hamburg. The structure was determined by molecular replacement using as a search model the 'blue-green' dimer of the bovine Cu,Zn superoxide dismutase. The crystallographic refinement of the molecular replacement solution was performed by means of molecular dynamics techniques and resulted in an R factor of 0.268 for the data between 6.0 and 2.5 A. The model was subsequently subjected to conventional restrained crystallographic refinement of the coordinates and temperature factors. The current R value for the data between 6.0 and 2.5 A is 0.220. Owing to the large radius of convergence of the molecular dynamics-crystallographic refinement, the convergence of the refinement process was reached after 18.1 ps of simulation time. The geometry of the active site of the enzyme appears essentially preserved compared with the bovine superoxide dismutase. The beta-barrel structure in the yeast enzyme is closed at the upper part by an efficient hydrogen-bonding scheme.

PubMed: 1772629
DOI: 10.1107/S0108768191004949

Experimental method

X-RAY DIFFRACTION (2.5 Å)