9K8U | pdb_00009k8u

Ethanol dehydrogenase of Bursaphelenchus xylophilus

• PDB DOI: https://doi.org/10.2210/pdb9K8U/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bursaphelenchus xylophilus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2024-10-24 Released: 2025-10-29 
• Deposition Author(s): Xing, Z.F., Luo, X., Li, X.Y., Song, R.J., Song, B.A.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.298 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: experimental

Literature

Ethanol dehydrogenase of Bursaphelenchus xylophilus

Xing, Z.F.

To be published.

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: 150.46 kDa 
• Atom Count: 10,504 
• Modeled Residue Count: 1,387 
• Deposited Residue Count: 1,388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alcohol dehydrogenase	A, B, C, D	347	Bursaphelenchus xylophilus	Mutation(s): 0  Gene Names: BXYJ_LOCUS12742 EC: 1.1.1.1
UniProt
Find proteins for A0A1I7RMX2 (Bursaphelenchus xylophilus) Explore A0A1I7RMX2  Go to UniProtKB:  A0A1I7RMX2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.298 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.707	α = 90
b = 152.773	β = 95.73
c = 63.792	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: 2025-10-29 
Deposition Author(s): Xing, Z.F., Luo, X., Li, X.Y., Song, R.J., Song, B.A.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32172457

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release