1IWA

RUBISCO FROM GALDIERIA PARTITA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 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

  • DOI: https://doi.org/10.1016/s0014-5793(02)03148-4
  • Primary Citation of Related Structures:  
    1IWA

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
A, C, E, G, I
A, C, E, G, I, K, M, O
493Galdieria partitaMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for O98949 (Galdieria partita)
Explore O98949 
Go to UniProtKB:  O98949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO98949
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
B, D, F, H, J
B, D, F, H, J, L, N, P
138Galdieria partitaMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for O98950 (Galdieria partita)
Explore O98950 
Go to UniProtKB:  O98950
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO98950
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.327α = 90
b = 146.988β = 99.79
c = 197.233γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations