Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 66.14 kDa 
• Atom Count: 4399 
• Residue Count: 516 
• Unique protein chains: 1

3P12

Crystal Structure of D-ribose Pyranase Sa240

• DOI: 10.2210/pdb3P12/pdb

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-29 Released: 2011-05-25 
• Deposition Author(s): Wu, M., Wang, L., Zang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.252 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

Crystal structure of Sa240: A ribose pyranase homolog with partial active site from Staphylococcus aureus

Wang, L., Wu, M., Zang, J.

(2011) J Struct Biol 174: 413-419

• PubMed: 21276853 
• DOI: 10.1016/j.jsb.2011.01.007
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Ribose is transported into cells in its pyranose form and must be rearranged to its furanose form for further utilization. Ribose pyranase RbsD catalyzes the conversion of ribose from the pyranose to furanose form. This is the key step for substrate supply to ribokinase RbsK, which converts ribose to ribose-5-phosphate for further metabolism. Sequence analysis indicated Sa240 from Staphylococcus aureus was a ribose pyranase homolog. Here we showed that Sa240 formed dimeric structure both in solution and in crystal. S240-ribose complex structure showed a ribose binding site formed by an incomplete active site compared with RbsD. Because the catalytic activity of ribose pyranase depends on its oligomeric state, we propose Sa240 is catalytically inactive in its dimeric structure.

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Organizational Affiliation: 

School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
D-ribose pyranase	A, B, C, D	144	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: rbsD, SAOUHSC_00240 EC: 5.5.1 (PDB Primary Data), 5.4.99.62 (UniProt)
Find proteins for Q2G1A5 (Staphylococcus aureus (strain NCTC 8325)) Explore Q2G1A5  Go to UniProtKB:  Q2G1A5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B, C, D	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.252 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.126	α = 90
b = 122.126	β = 90
c = 175.861	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-29 
• Released Date: 2011-05-25 
Deposition Author(s): Wu, M., Wang, L., Zang, J.

Revision History 

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance