1GEH

CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)

• PDB DOI: https://doi.org/10.2210/pdb1GEH/pdb

• Classification: LYASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-11-13 Released: 2001-12-19 
• Deposition Author(s): Kitano, K., Maeda, N., Fukui, T., Atomi, H., Imanaka, T., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.224 

Literature

Crystal Structure of a Novel-Type Archaeal Rubisco with Pentagonal Symmetry

Kitano, K., Maeda, N., Fukui, T., Atomi, H., Imanaka, T., Miki, K.

(2001) Structure 9: 473-481

• PubMed: 11435112 
• DOI: https://doi.org/10.1016/s0969-2126(01)00608-6
• Primary Citation of Related Structures:  
  1GEH


• PubMed Abstract: 
  

  Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2 fixation in plants, algae, and bacteria. Rubiscos have been so far classified into two types. Type I is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II is usually composed only of two L subunits (L2). Recently, some genuinely active Rubiscos of unknown physiological function have been reported from archaea.

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Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 249.84 kDa 
• Atom Count: 16,940 
• Modelled Residue Count: 2,135 
• Deposited Residue Count: 2,220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE	A, B, C, D, E	444	Thermococcus kodakarensis KOD1	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for O93627 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore O93627  Go to UniProtKB:  O93627

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D], N [auth E], O [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.224 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 233.75	α = 90
b = 233.75	β = 90
c = 93.26	γ = 120

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-19 
Deposition Author(s): Kitano, K., Maeda, N., Fukui, T., Atomi, H., Imanaka, T., Miki, K.

Revision History  

• Version 1.0: 2001-12-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations