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)

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
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Ligand Structure Quality Assessment

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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E6SHQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D5F (Subject of Investigation/LOI) Query on A1D5F Download:Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	4-oxidanylbutyl ~{N}-[4-[(4-aminophenyl)methyl]phenyl]carbamate C₁₈ H₂₂ N₂ O₃ UWOCPQGJYMGPEI-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

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: 2025-01-15
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.