8YMA | pdb_00008yma

CRYSTAL STRUCTURE OF A NOVEL PU PLASTIC DEGRADATION ENZYME FROM THERMAEROBACTER MARIANENSIS

PDB DOI: https://doi.org/10.2210/pdb8YMA/pdb

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

Deposited: 2024-03-08 Released: 2025-03-12
Deposition Author(s): Li, Z.S., Wang, H., Gao, J., Chen, Y.Y., Wei, H.L., Han, X., Wei, R., Bornscheuer, U.T., Liu, W.D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.227 (Depositor), 0.231 (DCC)
R-Value Work:
0.182 (Depositor), 0.196 (DCC)
R-Value Observed:
0.184 (Depositor)

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

Validation slider image for 8YMA

This is version 1.0 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF A NOVEL PU PLASTIC DEGRADATION ENZYME FROM THERMAEROBACTER MARIANENSIS

Li, Z.S., Wang, H., Gao, J., Chen, Y.Y., Wei, H.L., Han, X., Wei, R., Bornscheuer, U.T., Liu, W.D.

To be published.

Macromolecule Content

Total Structure Weight: 225.66 kDa
Atom Count: 15,377
Modeled Residue Count: 1,981
Deposited Residue Count: 2,108
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylic ester hydrolase	A, B, C, D	527	Thermaerobacter marianensis	Mutation(s): 0 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.227 (Depositor), 0.231 (DCC)
R-Value Work: 0.182 (Depositor), 0.196 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.834	α = 90
b = 81.834	β = 90
c = 667.371	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Bornscheuer, U.T.

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

Revision History (Full details and data files)

Version 1.0: 2025-03-12
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.