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)

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
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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

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

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidase	A, B	461	Sphingomonas sp. TPD3009	Mutation(s): 0 Gene Names: DC425_12480 EC: 3.5.1.4
UniProt
Find proteins for A0AAW3TV02 (Sphingomonas aquatilis) Explore A0AAW3TV02 Go to UniProtKB: A0AAW3TV02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAW3TV02
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

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

Revision History (Full details and data files)

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