9KOE | pdb_00009koe

X-ray crystallography of ascorbate peroxidase APEX2

• PDB DOI: https://doi.org/10.2210/pdb9KOE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Glycine max
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-11-20 Released: 2026-04-01 
• Deposition Author(s): Ke, M., Tian, R.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallography of ascorbate peroxidase APEX2

Ke, M., Tian, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 55.22 kDa 
• Atom Count: 4,195 
• Modeled Residue Count: 494 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ascorbate peroxidase	A, B	247	Glycine max	Mutation(s): 4  Gene Names: apx1 EC: 1.11.1.11
UniProt
Find proteins for Q43758 (Glycine max) Explore Q43758  Go to UniProtKB:  Q43758

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PO4	D [auth A], E [auth A], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.403	α = 90
b = 119.403	β = 90
c = 85.111	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-01 
Deposition Author(s): Ke, M., Tian, R.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92253304
National Natural Science Foundation of China (NSFC)	China	22125403

Revision History  

• Version 1.0: 2026-04-01
  Type: Initial release