› 2d69

X-ray diffraction
1.9Å resolution

Crystal structure of the complex of sulfate ion and octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Pyrococcus horikoshii OT3 (form-2 crystal)

Released:
DOI: 10.2210/pdb2d69/pdb
PDB entry 2d69 coloured by chain, front view.
PDB entry 2d69 coloured by chain, side view.
PDB entry 2d69 coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Entry authors: Mizohata E, Mishima C, Akasaka R, Uda H, Terada T, Shirouzu M, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assemblies composition:
homo octamer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129749 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribulose bisphosphate carboxylase Chains: A, B, D, E
Molecule details ›
Chains: A, B, D, E
Length: 430 amino acids
Theoretical weight: 48.31 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O58677 (Residues: 1-430; Coverage: 100%)
Gene names: PH0939, rbcL
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand SO4 19 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: C2
Unit cell:
a: 172.591Å b: 148.774Å c: 108.452Å
α: 90° β: 126.49° γ: 90°
R-values:
R R work R free
0.181 0.18 0.209
Expression system: Escherichia coli BL21(DE3)

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