8WDM | pdb_00008wdm

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

PDB DOI: https://doi.org/10.2210/pdb8WDM/pdb

Classification: HYDROLASE
Organism(s): Thermaerobacter marianensis DSM 12885
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-15 Released: 2024-09-18
Deposition Author(s): Li, Z.S., Wang, H., Gao, J., Chen, Y.Y., Wei, H.L., Li, Q., Han, X., Wei, R., Liu, W.D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.265 (Depositor), 0.262 (DCC)
R-Value Work:
0.231 (Depositor), 0.235 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: in silico
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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., Li, Q., Han, X., Wei, R., Liu, W.D.

To be published.

Macromolecule Content

Total Structure Weight: 225.57 kDa
Atom Count: 15,446
Modeled Residue Count: 1,981
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): 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.265 (Depositor), 0.262 (DCC)
R-Value Work: 0.231 (Depositor), 0.235 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.879	α = 90
b = 81.879	β = 90
c = 667.347	γ = 120

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: 2024-09-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371530

Revision History (Full details and data files)

Version 1.0: 2024-09-18
Type: Initial release