4HHH

Structure of Pisum sativum Rubisco


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

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This is version 1.2 of the entry. See complete history


Literature

Structure of Pisum sativum Rubisco with bound ribulose 1,5-bisphosphate.

Loewen, P.C.Didychuk, A.L.Switala, J.Perez-Luque, R.Fita, I.Loewen, M.C.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 10-14

  • DOI: 10.1107/S1744309112047549
  • Primary Citation of Related Structures:  
    4HHH

  • PubMed Abstract: 
  • The first structure of a ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from a pulse crop is reported. Rubisco was purified from Pisum sativum (garden pea) and diffraction-quality crystals were obtained by hanging-drop vapour diffusion in the presence of the substrate ribulose 1,5-bisphosphate ...

    The first structure of a ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from a pulse crop is reported. Rubisco was purified from Pisum sativum (garden pea) and diffraction-quality crystals were obtained by hanging-drop vapour diffusion in the presence of the substrate ribulose 1,5-bisphosphate. X-ray diffraction data were recorded to 2.20 Å resolution from a single crystal at the Canadian Light Source. The overall quaternary structure of non-activated P. sativum Rubisco highlights the conservation of the form I Rubisco hexadecameric complex. The electron density places the substrate in the active site at the interface of the large-subunit dimers. Lys201 in the active site is not carbamylated as expected for this non-activated structure. Some heterogeneity in the small-subunit sequence is noted, as well as possible variations in the conformation and contacts of ribulose 1,5-bisphosphate in the large-subunit active sites. Overall, the active-site conformation most closely correlates with the `closed' conformation observed in other substrate/inhibitor-bound Rubisco structures.


    Organizational Affiliation

    Department of Microbiology, University of Manitoba, 418 Buller Building, Winnipeg, MB R3T 2N2, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chainA, B, C, D475Pisum sativumMutation(s): 0 
Gene Names: rbcL
EC: 4.1.1.39
UniProt
Find proteins for P04717 (Pisum sativum)
Explore P04717 
Go to UniProtKB:  P04717
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04717
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small chainE [auth S],
F [auth T],
G [auth U],
H [auth V]
123Pisum sativumMutation(s): 0 
Gene Names: RBCS.3A
UniProt
Find proteins for P07689 (Pisum sativum)
Explore P07689 
Go to UniProtKB:  P07689
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07689
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RUB
Query on RUB

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
K [auth C],
L [auth D]
RIBULOSE-1,5-DIPHOSPHATE
C5 H12 O11 P2
YAHZABJORDUQGO-NQXXGFSBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.79α = 90
b = 109.95β = 90
c = 201.44γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CLSIdata collection
MOSFLMdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2013-01-23
    Changes: Database references