9KOJ | pdb_00009koj

Crystal structure of the isomerase Art22

• PDB DOI: https://doi.org/10.2210/pdb9KOJ/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-20 Released: 2025-07-30 
• Deposition Author(s): Guo, L., Li, P.W., Li, D.F., Chen, Y.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.203 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: in silico

Literature

Oxidative cleavage of hexopyranose by a TIM-barrel isomerase

Li, P., Wang, D., Guo, L., Chen, Y., Mao, H., Zhao, Z., Wang, M., Chen, M., Xu, Z., Wang, B., Li, D., Chen, Y.

(2025) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-025-01412-8

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.45 kDa 
• Atom Count: 4,788 
• Modeled Residue Count: 556 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Art22	A, B	299	Bacillus subtilis	Mutation(s): 0
UniProt
Find proteins for A0A317KV93 (Gracilibacillus dipsosauri) Explore A0A317KV93  Go to UniProtKB:  A0A317KV93

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.203 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.46	α = 90
b = 78.005	β = 90
c = 150.398	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Guo, L., Li, P.W., Li, D.F., Chen, Y.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32370042
National Natural Science Foundation of China (NSFC)	China	32025002

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release
  
• Version 1.1: 2025-10-22
  Changes: Database references