8RUC

ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 160-174

  • DOI: 10.1006/jmbi.1996.0310
  • Primary Citation of Related Structures:  
    8RUC

  • PubMed Abstract: 
  • Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from spinach is a hexadecamer (L8S8, Mr = 550,000) consisting of eight large (L, 475 residues) and eight small subunits (S, 123 residues). High-resolution data collection on crystals with larg ...

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from spinach is a hexadecamer (L8S8, Mr = 550,000) consisting of eight large (L, 475 residues) and eight small subunits (S, 123 residues). High-resolution data collection on crystals with large unit cells is not a trivial task due to the effect of radiation damage and the large number of overlapping reflections when conventional data collection methods are used. In order to minimise these effects, data on rubisco were collected with a giant Weissenberg camera at long crystal to image-plate distances at the synchrotron of the Photon Factory, Japan. Relative to conventional data sets, this experimental arrangement allowed a 20 to 30-fold reduction of the X-ray dose/exposure time for data collection. This paper describes the refined 1.6 A crystal structure of activated rubisco complexed with a transition state analogue, 2-carboxyarabinitol-bisphosphate. The crystallographic asymmetric unit contains an L4S4 unit, representing half of the molecule. The structure presented here is currently the highest resolution structure for any protein of comparable size. Refinement of the model was carried out by restrained least squares techniques without non-crystallographic symmetry averaging. The results show that all L and S subunits have identical three-dimensional structures, and their arrangement within the hexadecamer has no intrinsic asymmetry. A detailed analysis of the high-resolution maps identified 30 differences in the sequence of the small subunit, indicating a larger than usual heterogeneity for this nuclear encoded protein in spinach. No such differences were found in the sequence of the chloroplast encoded large subunit. The transition state analogue is in the cis conformation at the active site suggesting a key role for the carbamate of Lys201 in catalysis. Analysis of the active site around the catalytically essential magnesium ion further indicates that residues in the second liganding sphere of the metal play a role in fine-tuning the acid-base character and the position of the residues directly liganded to the metal.


    Related Citations: 
    • Crystallographic Analysis of Ribulose 1,5-Bisphosphate Carboxylase from Spinach at 2.4 A Resolution
      Knight, S., Andersson, I., Branden, C.I.
      (1990) J Mol Biol 215: 113
    • Crystal Structure of the Active Site of Ribulose-Bisphosphate Carboxylase
      Andersson, I., Knight, S., Schneider, G., Lindqvist, Y., Lundqvist, T., Branden, C.-I., Lorimer, G.H.
      (1989) Nature 337: 229
    • Reexamination of the Three-Dimensional Structure of the Small Subunit of Rubisco from Higher Plants
      Knight, S., Andersson, I., Branden, C.-I.
      (1989) Science 244: 702

    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASEACEG475Spinacia oleraceaMutation(s): 0 
Gene Names: rbcL
EC: 4.1.1.39
Find proteins for P00875 (Spinacia oleracea)
Explore P00875 
Go to UniProtKB:  P00875
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASEIJKL123Spinacia oleraceaMutation(s): 0 
Gene Names: RBCS
EC: 4.1.1.39
Find proteins for P00870 (Spinacia oleracea)
Explore P00870 
Go to UniProtKB:  P00870
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAP
Query on CAP

Download CCD File 
A, C, E, G
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, C, E, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A,C,E,GL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.2α = 90
b = 157.2β = 90
c = 201.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
SCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance