5WSK | pdb_00005wsk

Structure of Ribulose-1,5-bisphosphate carboxylase/oxygenase from wheat

• PDB DOI: https://doi.org/10.2210/pdb5WSK/pdb

• Classification: LYASE
• Organism(s): Triticum aestivum
• Mutation(s): No 


• Deposited: 2016-12-07 Released: 2018-02-14 
• Deposition Author(s): Ma, Y., Liu, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Structure of Ribulose-1,5-bisphosphate carboxylase/oxygenase from wheat

Ma, Y., Liu, C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 290 kDa 
• Atom Count: 19,532 
• Modeled Residue Count: 2,246 
• Deposited Residue Count: 2,608 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase large chain	A, B, C, D	477	Triticum aestivum	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for P11383 (Triticum aestivum) Explore P11383  Go to UniProtKB:  P11383

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase small chain	E, F, G [auth H], H [auth G]	175	Triticum aestivum	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for W5F0E6 (Triticum aestivum) Explore W5F0E6  Go to UniProtKB:  W5F0E6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	I [auth A], J [auth B], K [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.72	α = 90
b = 110.72	β = 90
c = 200.956	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Ma, Y., Liu, C.

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection