8XTB | pdb_00008xtb

Crystal structure of a novel PU plastic degradation urethanase UMG-SP2 from uncultured bacterium in complex with ligand

PDB DOI: https://doi.org/10.2210/pdb8XTB/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-01-10 Released: 2025-01-15
Deposition Author(s): Cong, L., Li, Z.S., Zheng, Z.R., Han, X., Wei, R., Liu, W.D., Uwe, B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.242 (Depositor), 0.246 (DCC)
R-Value Work:
0.207 (Depositor), 0.214 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a novel PU plastic degradation urethanase UMG-SP2 mutant from uncultured bacterium

Cong, L., Li, Z.S., Zheng, Z.R., Han, X., Wei, R., Liu, W.D., Uwe, B.

To be published.

Macromolecule Content

Total Structure Weight: 94.54 kDa
Atom Count: 6,637
Modeled Residue Count: 876
Deposited Residue Count: 908
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
umgsp2	A, B	454	uncultured bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D5H (Subject of Investigation/LOI) Query on A1D5H Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	4-oxidanylbutyl ~{N}-(4-aminophenyl)carbamate C₁₁ H₁₆ N₂ O₃ UEFKPOWGEZOFJI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.242 (Depositor), 0.246 (DCC)
R-Value Work: 0.207 (Depositor), 0.214 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.936	α = 90
b = 84.936	β = 90
c = 275.819	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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
Version 1.1: 2025-02-19
Changes: Data collection

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.