7W1J

Crystal structure of carboxylesterase from Thermobifida fusca with J1K

PDB DOI: https://doi.org/10.2210/pdb7W1J/pdb

Classification: HYDROLASE
Organism(s): Thermobifida fusca
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-19 Released: 2022-11-23
Deposition Author(s): Han, X., Gerlis, H., Li, Z., Gao, J., Wei, R., Liu, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.219
R-Value Work: 0.180
R-Value Observed: 0.182

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization

Von Haugwitz, G., Han, X., Pfaff, L., Li, Q., Wei, H., Gao, J., Methling, K., Ao, Y., Brack, Y., Mican, J., Feiler, C.G., Weiss, M.S., Bednar, D., Palm, G.J., Lalk, M., Lammers, M., Damborsky, J., Weber, G., Liu, W., Bornscheuer, U.T., Wei, R.

(2022) ACS Catal 12: 15259-15270

DOI: https://doi.org/10.1021/acscatal.2c03772

Macromolecule Content

Total Structure Weight: 53.2 kDa
Atom Count: 4,179
Modelled Residue Count: 494
Deposited Residue Count: 497
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylesterase	A	497	Thermobifida fusca	Mutation(s): 0 EC: 3.1.1.1
UniProt
Find proteins for P86325 (Thermobifida fusca) Explore P86325 Go to UniProtKB: P86325
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P86325
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J1K (Subject of Investigation/LOI) Query on J1K Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(2-hydroxyethylcarbamoyl)benzoic acid C₁₀ H₁₁ N O₄ HGTVOBHNUAVYMK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.219
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.438	α = 90
b = 79.943	β = 90
c = 113.007	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-11-23
Type: Initial release
Version 1.1: 2023-06-07
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

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.