8QJ0

Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO

• PDB DOI: https://doi.org/10.2210/pdb8QJ0/pdb

• Classification: LYASE
• Organism(s): Spinacia oleracea
• Mutation(s): No 


• Deposited: 2023-09-12 Released: 2024-05-29 
• Deposition Author(s): Bjelcic, M., Neutze, R., Aurelius, O., Nan, J., Ursby, T.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.181 

Starting Model: experimental

Literature

Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO.

Bjelcic, M., Aurelius, O., Nan, J., Neutze, R., Ursby, T.

(2024) Acta Crystallogr F Struct Biol Commun 80: 117-124

• PubMed: 38809540 
• DOI: https://doi.org/10.1107/S2053230X24004643
• Primary Citation of Related Structures:  
  8QJ0


• PubMed Abstract: 
  

  Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the enzyme responsible for the first step of carbon dioxide (CO ₂ ) fixation in plants, which proceeds via the carboxylation of ribulose 1,5-biphosphate. Because of the enormous importance of this reaction in agriculture and the environment, there is considerable interest in the mechanism of fixation of CO ₂ by RuBisCO. Here, a serial synchrotron crystallography structure of spinach RuBisCO is reported at 2.3 Å resolution. This structure is consistent with earlier single-crystal X-ray structures of this enzyme and the results are a good starting point for a further push towards time-resolved serial synchrotron crystallography in order to better understand the mechanism of the reaction.

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Organizational Affiliation: 

MAX IV Laboratory, Lund University, PO Box 118, 221 00 Lund, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 270.19 kDa 
• Atom Count: 18,884 
• Modelled Residue Count: 2,248 
• Deposited Residue Count: 2,392 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase small subunit, chloroplastic 2	A [auth S], B [auth T], C [auth U], D [auth V]	123	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for Q43832 (Spinacia oleracea) Explore Q43832  Go to UniProtKB:  Q43832

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase large chain	E [auth L], F [auth M], G [auth N], H [auth O]	475	Spinacia oleracea	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for P00875 (Spinacia oleracea) Explore P00875  Go to UniProtKB:  P00875

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	I [auth L], J [auth M], K [auth N], L [auth O]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	E [auth L], F [auth M], G [auth N], H [auth O]	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.181 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.6	α = 90
b = 157.12	β = 90
c = 202.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Bjelcic, M., Neutze, R., Aurelius, O., Nan, J., Ursby, T.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Database references
• Version 1.2: 2024-07-03
  Changes: Database references