Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Hetero 16-mer - A8B8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 271.37 kDa 
• Atom Count: 19680 
• Modelled Residue Count: 2324 
• Deposited Residue Count: 2392 
• Unique protein chains: 2

4HHH

Structure of Pisum sativum Rubisco

• DOI: 10.2210/pdb4HHH/pdb

• Classification: LYASE
• Organism(s): Pisum sativum
• Mutation(s): No 


• Deposited: 2012-10-09 Released: 2012-10-31 
• Deposition Author(s): Loewen, P.C., Didychuk, A.L., Switala, J., Loewen, M.C.

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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 

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

• PubMed: 23295478 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase large chain	A, B, C, D	475	Pisum sativum	Mutation(s): 0  Gene Names: rbcL EC: 4.1.1.39
Find proteins for P04717 (Pisum sativum) Explore P04717  Go to UniProtKB:  P04717

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase small chain	E [auth S], F [auth T], G [auth U], H [auth V]	123	Pisum sativum	Mutation(s): 0  Gene Names: RBCS-3A EC: 4.1.1.39
Find proteins for P07689 (Pisum sativum) Explore P07689  Go to UniProtKB:  P07689

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RUB	I [auth A], J [auth B], K [auth C], L [auth D]	RIBULOSE-1,5-DIPHOSPHATE C5 H12 O11 P2 YAHZABJORDUQGO-NQXXGFSBSA-N

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 = 109.79	α = 90
b = 109.95	β = 90
c = 201.44	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CLSI	data collection
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-09 
• Released Date: 2012-10-31 
Deposition Author(s): Loewen, P.C., Didychuk, A.L., Switala, J., Loewen, M.C.

Revision History  

• 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