7DZ3 | pdb_00007dz3

Crystal structures of D-allulose 3-epimerase with D-fructose from Sinorhizobium fredii

• PDB DOI: https://doi.org/10.2210/pdb7DZ3/pdb

• Classification: ISOMERASE
• Organism(s): Sinorhizobium fredii CCBAU 83666
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-23 Released: 2022-08-03 
• 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: 1.88 Å
• R-Value Free: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening

Li, C., Gao, X., Qi, H., Zhang, W., Li, L., Wei, C., Wei, M., Sun, X., Wang, S., Wang, L., Ji, Y., Mao, S., Zhu, Z., Tanokura, M., Lu, F., Qin, H.M.

(2023) Angew Chem Int Ed Engl 

• DOI: https://doi.org/10.1002/anie.202216721

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 125.8 kDa 
• Atom Count: 9,151 
• Modeled Residue Count: 1,136 
• Deposited Residue Count: 1,144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tagatose 3-epimerase	A, B, C, D	286	Sinorhizobium fredii CCBAU 83666	Mutation(s): 0  Gene Names: SF83666_b55120 EC: 5.1.3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.437	α = 90
b = 120.648	β = 90
c = 134.633	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: 2022-08-03 
Deposition Author(s): Zhu, Z.L., Miyakawa, T., Tanokura, M., Lu, F.P., Qin, H.-M.

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2023-02-15
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description