1GOX

REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION

Summary for 1GOX

• Entry DOI: 10.2210/pdb1gox/pdb
• Descriptor: (S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL, FLAVIN MONONUCLEOTIDE (3 entities in total)
• Functional Keywords: oxidoreductase (oxygen(a))
• Biological source: Spinacia oleracea (spinach)
• Cellular location: Peroxisome: P05414
• Total number of polymer chains: 1
• Total formula weight: 40815.89

Authors

Lindqvist, Y. (deposition date: 1989-06-14, release date: 1989-10-15, Last modification date: 2024-11-20)

Primary citation

Lindqvist, Y.
Refined structure of spinach glycolate oxidase at 2 A resolution.
J.Mol.Biol., 209:151-166, 1989

PubMed Abstract: The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 independent reflections from 5.5 to 2 A resolution. The geometry of the model, consisting of 350 amino acid residues, the cofactor flavin mononucleotide and 298 solvent molecules, is close to ideal with root-mean-square deviations of 0.015 A in bond lengths and 2.6 degrees in bond angles. The expected trimodal distribution with preference for staggered conformation is obtained for the side-chain chi 1-angles. The core of the subunit is built up from the eight beta-strands in the beta/alpha-barrel. This core consists of two hydrophobic layers. One in the center is made up of residues pointing in from the beta-strands towards the barrel axis and the second, consisting of two segments of residues, pointing out from the beta-strands towards the eight alpha-helices of the barrel and pointing from the helices towards the strands. The hydrogen bond pattern for the beta-strands in the beta/alpha-barrel is described. There are a number of residues with 3(10)-helix conformation, in particular there is one left-handed helix. The ordered solvent molecules are organized mainly in clusters. The average isotropic temperature factor is quite high, 27.1 A2, perhaps a reflection of the high solvent content in the crystal. The octameric glycolate oxidase molecule, which has 422 symmetry, makes strong interactions around the 4-fold axis forming a tight tetramer, but only weak interactions between the two tetramers forming the octamer.

PubMed: 2681790
DOI: 10.1016/0022-2836(89)90178-2

Experimental method

X-RAY DIFFRACTION (2 Å)