8XRZ | pdb_00008xrz

Crystal structure of a novel PU plastic degradation enzyme with ligand from Thermaerobacter marianensis

• PDB DOI: https://doi.org/10.2210/pdb8XRZ/pdb

• Classification: HYDROLASE
• Organism(s): Thermaerobacter marianensis DSM 12885
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2024-01-08 Released: 2025-01-15 
• Deposition Author(s): Li, Z.S., Wang, H., Zheng, Z.R., Cong, L., Chen, Y.Y., Han, X., Wei, R., Uwe, B., 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: 2.11 Å
• R-Value Free: 
  0.225 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a novel PU plastic degradation enzyme with ligand from Thermaerobacter marianensis

Li, Z.S., Wang, H., Zheng, Z.R., Cong, L., Chen, Y.Y., Han, X., Wei, R., Uwe, B., liu, W.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 225.91 kDa 
• Atom Count: 15,514 
• Modeled Residue Count: 1,980 
• Deposited Residue Count: 2,108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylic ester hydrolase	A, B, C, D	527	Thermaerobacter marianensis DSM 12885	Mutation(s): 1  Gene Names: Tmar_0630 EC: 3.1.1
UniProt
Find proteins for E6SHQ4 (Thermaerobacter marianensis (strain ATCC 700841 / DSM 12885 / JCM 10246 / 7p75a)) Explore E6SHQ4  Go to UniProtKB:  E6SHQ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D5F (Subject of Investigation/LOI)	F [auth C]	4-oxidanylbutyl ~{N}-[4-[(4-aminophenyl)methyl]phenyl]carbamate C18 H22 N2 O3 UWOCPQGJYMGPEI-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.225 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.566	α = 90
b = 81.566	β = 90
c = 667.529	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Li, Z.S., Wang, H., Zheng, Z.R., Cong, L., Chen, Y.Y., Han, X., Wei, R., Uwe, B., 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: 2025-01-15
  Type: Initial release