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 1IWA | pdb_00001iwa

RUBISCO FROM GALDIERIA PARTITA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.235 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1IWA

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 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.

Macromolecule Content 

  • Total Structure Weight: 570.93 kDa 
  • Atom Count: 42,000 
  • Modeled Residue Count: 4,888 
  • Deposited Residue Count: 5,048 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
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:|  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 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
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