3P13

Complex Structure of D-ribose Pyranase Sa240 with D-ribose

• PDB DOI: https://doi.org/10.2210/pdb3P13/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: 0.250 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

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)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 66.38 kDa 
• Atom Count: 4,313 
• Modelled Residue Count: 518 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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
UniProt
Find proteins for Q2G1A5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G1A5  Go to UniProtKB:  Q2G1A5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIP	E [auth A], F [auth B], G [auth C], H [auth D]	beta-D-ribopyranose C5 H10 O5 SRBFZHDQGSBBOR-TXICZTDVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.250 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.27	α = 90
b = 124.27	β = 90
c = 86.21	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary