› 1wdd

X-ray diffraction
1.35Å resolution

Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate

Released:
DOI: 10.2210/pdb1wdd/pdb
PDB entry 1wdd coloured by chain, front view.
PDB entry 1wdd coloured by chain, side view.
PDB entry 1wdd 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 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, E
Molecule details ›
Chains: A, E
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, W
Molecule details ›
Chains: S, W
Length: 128 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

3 bound ligands:
Ligand MG 2 x MG
Ligand CAP 2 x CAP
Ligand GOL 17 x GOL
2 modified residues:
Ligand KCX 2 x KCX
Ligand MME 2 x MME

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: I4
Unit cell:
a: 111.713Å b: 111.713Å c: 196.78Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.16 0.182

Quick links

Citations

2 review citations

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

12 mentions without citation

Red Rubiscos and opportunities for engineering green plants.
Oh et al. (2023)
11 more