1TQJ

Crystal structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb1TQJ/pdb

• Classification: ISOMERASE
• Organism(s): Synechocystis sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-17 Released: 2004-08-31 
• Deposition Author(s): Wise, E.L., Akana, J., Gerlt, J.A., Rayment, I.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.220 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution.

Wise, E.L., Akana, J., Gerlt, J.A., Rayment, I.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1687-1690

• PubMed: 15333955 
• DOI: https://doi.org/10.1107/S0907444904015896
• Primary Citation of Related Structures:  
  1TQJ


• PubMed Abstract: 
  

  The crystal structure of D-ribulose 5-phosphate 3-epimerase (RPE) from the cyanobacterium Synechocystis was determined by X-ray crystallography to 1.6 A resolution. The enzyme, which catalyzes the epimerization of D-ribulose 5-phosphate and D-xylulose 5-phosphate, assembles as a hexamer of (beta/alpha)(8)-barrels in the crystallographic asymmetric unit. The active site is highly similar to those of two previously reported RPEs and provides further evidence for essential catalytic roles for several active-site residues.

---

Organizational Affiliation: 

Deparment of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 149.99 kDa 
• Atom Count: 11,308 
• Modelled Residue Count: 1,297 
• Deposited Residue Count: 1,380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose-phosphate 3-epimerase	A, B, C, D, E, F	230	Synechocystis sp.	Mutation(s): 0  Gene Names: RPE, SLL0807 EC: 5.1.3.1
UniProt
Find proteins for P74061 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74061  Go to UniProtKB:  P74061

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.220 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.564	α = 90
b = 87.779	β = 114.58
c = 97.821	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-31 
Deposition Author(s): Wise, E.L., Akana, J., Gerlt, J.A., Rayment, I.

Revision History  

• Version 1.0: 2004-08-31
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references