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PDBsum entry 8rub

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Lyase(carbon-carbon) PDB id
8rub
Jmol
Contents
Protein chains
123 a.a.
467 a.a.
Ligands
CAP
Metals
_MG

References listed in PDB file
Key reference
Title Crystallographic analysis of ribulose 1,5-Bisphosphate carboxylase from spinach at 2.4 a resolution. Subunit interactions and active site.
Authors S.Knight, I.Andersson, C.I.Brändén.
Ref. J Mol Biol, 1990, 215, 113-160. [DOI no: 10.1016/S0022-2836(05)80100-7]
PubMed id 2118958
Abstract
The X-ray structure of the quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase from spinach with CO2, Mg2+ and a reaction-intermediate analogue (CABP) has been determined and refined at 2.4 A resolution. Cyclic non-crystallographic symmetry averaging around the molecular 4-fold axis and phase combination were used to improve the initial multiple isomorphous replacement phases. A model composed of one large subunit and one small subunit was built in the resulting electron density map, which was of excellent quality. Application of the local symmetry gave an initial model of the L8S8 molecule with a crystallographic R-value of 0.43. Refinement of this initial model was performed by a combination of conventional least-squares energy refinement and molecular dynamics simulation using the XPLOR program. Three rounds of refinement, interspersed with manual rebuilding at the graphics display, resulted in a model containing all of the 123 amino acid residues in the small subunit, and 467 of the 475 residues in the large subunit. The R-value for this model is 0.24, with relatively small deviations from ideal stereochemistry. Subunit interactions in the L8S8 molecule have been analysed and are described. The interface areas between the subunits are extensive, and bury almost half of the accessible surface areas of both the large and the small subunit. A number of conserved interaction areas that may be of functional significance have been identified and are described, and biochemical and mutagenesis data are discussed in the structural framework of the model.
Secondary reference #1
Title Reexamination of the three-Dimensional structure of the small subunit of ruBisCo from higher plants
Authors S.Knight, I.Andersson, C.-I.Branden.
Ref. science, 1989, 244, 702.
Secondary reference #2
Title Crystal structure of the active site of ribulose-Bisphosphate carboxylase
Authors I.Andersson, S.Knight, G.Schneider, Y.Lindqvist, T.Lundqvist, C.-I.Branden, G.H.Lorimer.
Ref. nature, 1989, 337, 229.
PROCHECK
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