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Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate
1WDD
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Lyase
    Structure Weight: 138274.44
    Molecule: Ribulose bisphosphate carboxylase large chain
    Polymer: 1 Type: protein Length: 477
    Chains: A, E
    EC#: 4.1.1.39   
    Organism: Oryza sativa Japonica Group
    Gene Names: rbcL LOC_Osp1g00420 Nip064
    UniProtKB: Protein Feature View | Search PDB | P0C512  
    Molecule: Ribulose bisphosphate carboxylase small chain C
    Polymer: 2 Type: protein Length: 128
    Chains: S, W
    EC#: 4.1.1.39   
    Organism: Oryza sativa Japonica Group
    Gene Names: RBCS RBCS-C Os12g0274700 LOC_Os12g17600 OsJ_016909
    UniProtKB: Protein Feature View | Search PDB | Q0INY7  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Oryza sativa japonica group   Taxonomy   Common Name: Japanese rice  
    Polymer: 2
    Scientific Name: Oryza sativa japonica group   Taxonomy   Common Name: Japanese rice  
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    CAP
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    CAP C6 H14 O13 P2
    2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
    GOL
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    GOL C3 H8 O3
    GLYCEROL
    MG
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    MG Mg
    MAGNESIUM ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    KCX
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    KCX C7 H14 N2 O4 LYS lPeptideLinking
    MME
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    MME C6 H13 N O2 S MET lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA,PQS (software)
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  •   Deposition Summary Hide
    Authors:   Mizohata, E.,  Matsumura, H.,  Ueno, T.,  Ishida, H.,  Inoue, T.,  Makino, A.,  Mae, T.,  Kai, Y.

    Deposition:   2004-05-13
    Release:   2004-11-13
    Last Modified (REVDAT):   2013-06-05
     
  •   Revision History    Hide
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    2013-06-05
    Citation
    2012-06-13
    Citation
    2011-07-13
    Version format compliance
    2011-07-13
    Biological assembly
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.35
    R-Value: 0.160 (obs.)
    R-Free: 0.182
    Space Group: I 4
    Unit Cell:
      Length [Å] Angles [°]
    a = 111.71 α = 90.00 
    b = 111.71 β = 90.00 
    c = 196.78 γ = 90.00