1IWA

RUBISCO FROM GALDIERIA PARTITA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-Ray Structure of Galdieria Rubisco Complexed with one sulfate ion per active site

Okano, Y.Mizohata, E.Xie, Y.Matsumura, H.Sugawara, H.Inoue, T.Yokota, A.Kai, Y.

(2002) FEBS LETT. 527: 33-36


  • PubMed Abstract: 
  • Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the reactions of carboxylation and oxygenation of ribulose-1,5-bisphosphate. These reactions require that the active site should be closed by a flexible loop (loop 6) of the large su ...

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the reactions of carboxylation and oxygenation of ribulose-1,5-bisphosphate. These reactions require that the active site should be closed by a flexible loop (loop 6) of the large subunit. Rubisco from a red alga, Galdieria partita, has the highest specificity for carboxylation reaction among the Rubiscos hitherto reported. The crystal structure of unactivated Galdieria Rubisco has been determined at 2.6 A resolution. The electron density map reveals that a sulfate binds only to the P1 anion-binding site of the active site and the loop 6 is closed. Galdieria Rubisco has a unique hydrogen bond between the main chain oxygen of Val332 on the loop 6 and the epsilon-amino group of Gln386 of the same large subunit. This interaction is likely to be crucial to understanding for stabilizing the loop 6 in the closed state and to making a higher affinity for anionic ligands.


    Related Citations: 
    • The Transition between the Open and Closed States of Rubisco is triggered by the Inter-Phosphate Distance of the Bound Bisphosphate
      Duff, A.P.,Andrews, T.J.,Curmi, P.M.
      (2000) J.Mol.Biol. 298: 903


    Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
A, C, E, G, I, K, M, O
493Galdieria partitaN/A
Find proteins for O98949 (Galdieria partita)
Go to UniProtKB:  O98949
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
B, D, F, H, J, L, N, P
138Galdieria partitaGene Names: rbcS
Find proteins for O98950 (Galdieria partita)
Go to UniProtKB:  O98950
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 201.327α = 90.00
b = 146.988β = 99.79
c = 197.233γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance