7ERO

Crystal structure of D-allulose 3-epimerase with D-allulose from Agrobacterium sp. SUL3

• PDB DOI: https://doi.org/10.2210/pdb7ERO/pdb

• Classification: ISOMERASE
• Organism(s): Agrobacterium sp. SUL3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-06 Released: 2022-05-11 
• Deposition Author(s): Zhu, Z.L., Miyakawa, T., Tanokura, M., Lu, F.P., Qin, H.-M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.227 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Growth-Coupled Evolutionary Pressure Improving Epimerases for D-Allulose Biosynthesis Using a Biosensor-Assisted In Vivo Selection Platform

Li, C., Gao, H., Li, H., Wang, T., Lu, F.P., Qin, H.-M.

(2024) Adv Sci (Weinh) 

• DOI: https://doi.org/10.1002/advs.202306478

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 123.16 kDa 
• Atom Count: 8,995 
• Modelled Residue Count: 1,132 
• Deposited Residue Count: 1,136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tagatose 3-epimerase	A, B, C, D	284	Agrobacterium sp. SUL3	Mutation(s): 0  Gene Names: AKG12_23230 EC: 5.1.3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PSJ (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	D-psicose C6 H12 O6 BJHIKXHVCXFQLS-PUFIMZNGSA-N
MG (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.227 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.173	α = 90
b = 97.517	β = 90
c = 159.922	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-05-11 
Deposition Author(s): Zhu, Z.L., Miyakawa, T., Tanokura, M., Lu, F.P., Qin, H.-M.

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-02-07
  Changes: Database references