1BXN

THE CRYSTAL STRUCTURE OF RUBISCO FROM ALCALIGENES EUTROPHUS TO 2.7 ANGSTROMS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded beta-barrel formed by beta-strands from four subunits.

Hansen, S.Vollan, V.B.Hough, E.Andersen, K.

(1999) J Mol Biol 288: 609-621

  • DOI: https://doi.org/10.1006/jmbi.1999.2701
  • Primary Citation of Related Structures:  
    1BXN

  • PubMed Abstract: 

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is involved in photosynthesis where it catalyzes the initial step in the fixation of carbon dioxide. The enzyme also catalyzes a competing oxygenation reaction leading to loss of fixed carbon dioxide, thus reducing the net efficiency of photosynthesis significantly. Rubisco has therefore been studied extensively, and a challenging goal is the engineering of a more photosynthetically efficient enzyme. Hexadecameric rubiscos fall in two distinct groups, "green-like" and "red-like". The ability to discriminate between CO2 and O2 as substrates varies significantly, and some algae have red-like rubisco with even higher specificity for CO2 than the plant enzyme. The structure of unactivated rubisco from Alcaligenes eutrophus has been determined to 2.7 A resolution by molecular replacement and refined to R and Rfree values of 26.6 and 32.2 %, respectively. The overall fold of the protein is very similar to the rubisco structures solved previously for green-like hexadecameric enzymes, except for the extended C-terminal domains of the small subunits which together form an eight-stranded beta-barrel which sits as a plug in the entrance to the central solvent channel in the molecule. The present structure is the first which has been solved for a red-like rubisco and is likely to represent a fold which is common for this group. The small subunits in general are believed to have a stabilizing effect, and the new quaternary structure in the oligomer of the present structure is likely to contribute even more to this stabilization of the assembled rubisco protein.


  • Organizational Affiliation

    Department of Chemistry, University of Tromso, Tromso, N-9037, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
A, C, E, G
485Cupriavidus necatorMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for P0C2C2 (Cupriavidus necator)
Explore P0C2C2 
Go to UniProtKB:  P0C2C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C2C2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)B [auth I],
D [auth J],
F [auth K],
H [auth L]
139Cupriavidus necatorMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for P09658 (Cupriavidus necator)
Explore P09658 
Go to UniProtKB:  P09658
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09658
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112α = 90
b = 112β = 90
c = 402.7γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description