4GMK

Crystal Structure of Ribose 5-Phosphate Isomerase from the Probiotic Bacterium Lactobacillus salivarius UCC118

• PDB DOI: https://doi.org/10.2210/pdb4GMK/pdb

• Classification: ISOMERASE
• Organism(s): Ligilactobacillus salivarius UCC118
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-16 Released: 2012-08-29 
• Deposition Author(s): Lobley, C.M.C., Aller, P., Douangamath, A., Reddivari, Y., Bumann, M., Bird, L.E., Brandao-Neto, J., Owens, R.J., O'Toole, P.W., Walsh, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.206 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118.

Lobley, C.M., Aller, P., Douangamath, A., Reddivari, Y., Bumann, M., Bird, L.E., Nettleship, J.E., Brandao-Neto, J., Owens, R.J., O'Toole, P.W., Walsh, M.A.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1427-1433

• PubMed: 23192019 
• DOI: https://doi.org/10.1107/S174430911204273X
• Primary Citation of Related Structures:  
  4GMK


• PubMed Abstract: 
  

  The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β D-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography.

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Organizational Affiliation: 

Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 50.2 kDa 
• Atom Count: 3,844 
• Modelled Residue Count: 451 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-5-phosphate isomerase A	A, B	228	Ligilactobacillus salivarius UCC118	Mutation(s): 0  Gene Names: rpiA EC: 5.3.1.6
UniProt
Find proteins for Q1WR87 (Ligilactobacillus salivarius (strain UCC118)) Explore Q1WR87  Go to UniProtKB:  Q1WR87

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	E [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.206 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.34	α = 90
b = 63.8	β = 107.68
c = 59.84	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
REFMAC	refinement
xia2	data reduction
xia2	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Lobley, C.M.C., Aller, P., Douangamath, A., Reddivari, Y., Bumann, M., Bird, L.E., Brandao-Neto, J., Owens, R.J., O'Toole, P.W., Walsh, M.A.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations