› 3axm

X-ray diffraction
1.65Å resolution

Structure of rice Rubisco in complex with 6PG

Released:
DOI: 10.2210/pdb3axm/pdb
PDB entry 3axm coloured by chain, front view.
PDB entry 3axm coloured by chain, side view.
PDB entry 3axm coloured by chain, top view.
Source organism: Oryza sativa Japonica Group
Primary publication:
Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate.
Matsumura H, Mizohata E, Ishida H, Kogami A, Ueno T, Makino A, Inoue T, Yokota A, Mae T, Kai Y
J Mol Biol 422 75-86 (2012)
PMID: 22609438

Function and Biology Details

Reaction catalysed: 
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143016 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribulose bisphosphate carboxylase large chain Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 477 amino acids
Theoretical weight: 52.99 KDa
Source organism: Oryza sativa Japonica Group
UniProt:
  • Canonical: P0C512 (Residues: 1-477; Coverage: 100%)
Gene names: LOC_Osp1g00420, Nip064, rbcL
Sequence domains:
Structure domains:
Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 Chains: S, T, U, V, W, X, Y, Z
Molecule details ›
Chains: S, T, U, V, W, X, Y, Z
Length: 129 amino acids
Theoretical weight: 14.98 KDa
Source organism: Oryza sativa Japonica Group
UniProt:
  • Canonical: Q0INY7 (Residues: 48-175; Coverage: 73%)
Gene names: LOC_Os12g17600, Os12g0274700, OsJ_016909, OsJ_17688, RBCS, RBCS-C
Sequence domains: Ribulose bisphosphate carboxylase, small chain
Structure domains: Ribulose bisphosphate carboxylase, small subunit

Ligands and Environments

2 bound ligands:
Ligand MG 8 x MG
Ligand 6PG 8 x 6PG
1 modified residue:
Ligand KCX 8 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 110.408Å b: 199.624Å c: 111.169Å
α: 90° β: 91.45° γ: 90°
R-values:
R R work R free
0.171 0.171 0.19

Quick links

Citations

2 review citations

Photorespiration and nitrate assimilation: a major intersection between plant carbon and nitrogen.
Bloom AJ. (2015)
1 more

5 mentions without citation

Development of an activity-directed selection system enabled significant improvement of the carboxylation efficiency of Rubisco.
Cai et al. (2014)
4 more