1AA1

ACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGLYCERATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase.

Taylor, T.C.Andersson, I.

(1997) Biochemistry 36: 4041-4046

  • DOI: 10.1021/bi962818w
  • Primary Citation of Related Structures:  1AUS

  • PubMed Abstract: 
  • The crystal structure of an activated complex of ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach and its product 3-phosphoglycerate has been determined to 2.2 A resolution. The structure is of the open form with the active site accessibl ...

    The crystal structure of an activated complex of ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach and its product 3-phosphoglycerate has been determined to 2.2 A resolution. The structure is of the open form with the active site accessible to the solvent as observed in the structures of the activated ligand-free enzyme and the complex of the activated enzyme with the substrate ribulose-1,5-bisphosphate. Two molecules of 3-phosphoglycerate are bound per active site. The phosphates of both molecules bind approximately at the same position as the phosphates of ribulose-1,5-bisphosphate or the six-carbon intermediate analogue 2-carboxyarabinitol-1,5-bisphosphate, but one product molecule is swung out from the active site with its carboxylate group pointing toward solution. The present structure points to direct participation of the active site side chain of lysine 175 in later stages of catalysis. This possibility is discussed in the light of mutagenesis studies.


    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


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Scineces, Uppsala.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
L, B, E, H
475Spinacia oleraceaGene Names: rbcL
EC: 4.1.1.39
Find proteins for P00875 (Spinacia oleracea)
Go to UniProtKB:  P00875
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
S, C, F, I
123Spinacia oleraceaGene Names: RBCS2
EC: 4.1.1.39
Find proteins for Q43832 (Spinacia oleracea)
Go to UniProtKB:  Q43832
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, E, H, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3PG
Query on 3PG

Download SDF File 
Download CCD File 
B, E, H, L
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
B, E, H, L
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 157.600α = 90.00
b = 158.700β = 90.00
c = 203.300γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance