9KR3 | pdb_00009kr3

Structural Basis for the Polymer-Protein Binding Mechanism of Polyvinyl Alcohol Esterase

• PDB DOI: https://doi.org/10.2210/pdb9KR3/pdb

• Classification: HYDROLASE
• Organism(s): Comamonas sp. NyZ500
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-27 Released: 2025-10-08 
• Deposition Author(s): Wu, Y.F., Xu, X.X., Yin, C.F., Wang, L.T., Zhou, N.Y., Zhou, J.
• Funding Organization(s): National Key R&D Program of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: in silico

Literature

Structural Basis for the Enzyme-Polymer Binding Mechanism of Poly(vinyl alcohol) Esterase

Wu, Y., Xu, X., Yin, C.F., Shen, Z., Wang, L., Zhou, N.Y., Zhou, J.

(2025) ACS Catal 15: 11194-11203

• DOI: https://doi.org/10.1021/acscatal.5c01764

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.16 kDa 
• Atom Count: 3,615 
• Modeled Residue Count: 391 
• Deposited Residue Count: 403 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SGNH/GDSL hydrolase family protein	A	403	Comamonas sp. NyZ500	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EGL (Subject of Investigation/LOI)	B [auth A]	[(2S,4S,6S,8S,10R,12R,14R,16R,18R,20R)-12-acetyloxy-2,4,6,10,14,16,18,20,22-nonakis(oxidanyl)docosan-8-yl] ethanoate C26 H50 O13 KNZHZBPEWADAET-WIIBHWIMSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.79	α = 90
b = 164.79	β = 90
c = 164.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Wu, Y.F., Xu, X.X., Yin, C.F., Wang, L.T., Zhou, N.Y., Zhou, J.

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Funding Organization	Location	Grant Number
National Key R&D Program of China	China	2021YFA0909500

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release