2YBV

STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS

• PDB DOI: https://doi.org/10.2210/pdb2YBV/pdb

• Classification: LYASE
• Organism(s): Thermosynechococcus vestitus BP-1
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2011-03-10 Released: 2012-03-28 
• Deposition Author(s): Terlecka, B., Wilhelmi, V., Bialek, W., Gubernator, B., Szczepaniak, A., Hofmann, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.232 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Structure of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase from Thermosynechococcus Elongatus

Terlecka, B., Wilhelmi, V., Bialek, W., Gubernator, B., Szczepaniak, A., Hofmann, E.

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)

Macromolecule Content

• Total Structure Weight: 537.26 kDa 
• Atom Count: 34,583 
• Modelled Residue Count: 4,256 
• Deposited Residue Count: 4,744 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN	A, C, E, G, I, K, M, O	475	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for Q8DIS5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIS5  Go to UniProtKB:  Q8DIS5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT	B, D, F, H, J, L, N, P	118	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for Q8DIS7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIS7  Go to UniProtKB:  Q8DIS7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	AA [auth K], BA [auth M], CA [auth M], DA [auth O], EA [auth O], Q [auth A], R [auth A], S [auth C], T [auth C], U [auth E], V [auth G], W [auth G], X [auth I], Y [auth I], Z [auth K]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.232 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.48	α = 90
b = 163.47	β = 108.96
c = 163.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Terlecka, B., Wilhelmi, V., Bialek, W., Gubernator, B., Szczepaniak, A., Hofmann, E.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description