Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Hetero 16-mer - A8B8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 541.61 kDa 
• Atom Count: 39512 
• Residue Count: 4720 
• Unique protein chains: 2

1RCO

SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE

• DOI: 10.2210/pdb1RCO/pdb

• Classification: LYASE
• Organism(s): Spinacia oleracea
• Mutation(s): No 


• Deposited: 1996-10-31 Released: 1997-03-12 
• Deposition Author(s): Taylor, T.C., Andersson, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Literature

A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate.

Taylor, T.C., Fothergill, M.D., Andersson, I.

(1996) J Biol Chem 271: 32894-32899

• PubMed: 8955130 
• DOI: 10.1074/jbc.271.51.32894
• Primary Citation of Related Structures:  
  1RBO, 1RCO


• PubMed Abstract: 
  

Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the carboxylation of ribulose 1,5-bisphosphate. The reaction catalyzed by Rubisco involves several steps, some of which can occur as partial reactions, forming intermediates that can be isolated. Analogues of these intermediates are potent inhibitors of the enzyme. We have studied the interactions with the enzyme of two inhibitors, xylulose 1,5-bisphosphate and 4-carboxyarabinitol 1,5-bisphosphate, by x-ray crystallography. Crystals of the complexes were formed by cocrystallization under activating conditions. In addition, 4-carboxyarabinitol 1,5-bisphosphate was soaked into preformed activated crystals of the enzyme. The result of these experiments was the release of the activating CO2 molecule as well as the metal ion from the active site when the inhibitors bound to the enzyme. Comparison with the structure of an activated complex of the enzyme indicates that the structural basis for the release of the activator groups is a distortion of the metal binding site due to the different geometry of the C-3 hydroxyl of the inhibitors. Both inhibitors induce closure of active site loops despite the inactivated state of the enzyme. Xylulose 1,5-bisphosphate binds in a hydrated form at the active site.

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Related Citations: 

• Large Structures at High Resolution: The 1.6 A Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Complexed with 2-Carboxyarabinitol Bisphosphate
  Andersson, I.
  (1996) J Mol Biol 259: 160

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Organizational Affiliation: 

Department of Molecular Biology, Swedish University of Agricultural Sciences, P. O. Box 590, S-751 24 Uppsala, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE	B, E, H, K, L, O, R, V	475	Spinacia oleracea	Mutation(s): 0  Gene Names: rbcL EC: 4.1.1.39
Find proteins for P00875 (Spinacia oleracea) Explore P00875  Go to UniProtKB:  P00875

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE	C, F, I, M, P, S, T, W	123	Spinacia oleracea	Mutation(s): 0  Gene Names: RBCS EC: 4.1.1.39
Find proteins for P00870 (Spinacia oleracea) Explore P00870  Go to UniProtKB:  P00870

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XDP	B, E, H, K, L, O, R, V	D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE C5 H14 O12 P2 XXHQHBUKQCAIGV-DMTCNVIQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 220.6	α = 90
b = 221.7	β = 90
c = 115.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-10-31 
• Released Date: 1997-03-12 
Deposition Author(s): Taylor, T.C., Andersson, I.

Revision History 

• Version 1.0: 1997-03-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance