9JE9 | pdb_00009je9

Crystal structure of a amidase that can hydrolase PU plastic

• PDB DOI: https://doi.org/10.2210/pdb9JE9/pdb

• Classification: HYDROLASE
• Organism(s): Sphingomonas sp. TPD3009
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-09-02 Released: 2025-07-09 
• Deposition Author(s): Li, Z.S., Fang, S.T., Zheng, Z.R., Xia, W., Zhou, H.Y., Li, W.S., You, S., Han, X., Liu, W.D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: in silico

Literature

Discovery and Engineering of a Urethanase for Enhanced Depolymerization of Polyurethane

Li, Z., Fan, S., Chen, Y., Xia, W., Zhou, H., Zhou, X., Qin, B., Qin, H., Dong, W., Gu, Q., Zhu, H., Bornscheuer, U.T., Wei, R., Han, X., Liu, W.

(2025) ACS Catal 15: 10768-10779

• DOI: https://doi.org/10.1021/acscatal.5c01062

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 98.38 kDa 
• Atom Count: 6,299 
• Modeled Residue Count: 830 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidase	A, B	461	Sphingomonas sp. TPD3009	Mutation(s): 0  Gene Names: DC425_12480

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.82	α = 90
b = 92.82	β = 90
c = 135.086	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Li, Z.S., Fang, S.T., Zheng, Z.R., Xia, W., Zhou, H.Y., Li, W.S., You, S., Han, X., Liu, W.D.

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

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release