7E7L

The crystal structure of arylacetate decarboxylase from Olsenella scatoligenes.

PDB DOI: https://doi.org/10.2210/pdb7E7L/pdb

Classification: LYASE
Organism(s): Tractidigestivibacter scatoligenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-02-26 Released: 2021-07-28
Deposition Author(s): Lu, Q., Duan, Y., Zhang, Y., Yuchi, Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.53 Å
R-Value Free: 0.358
R-Value Work: 0.290
R-Value Observed: 0.295

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Glycyl Radical Enzyme Arylacetate Decarboxylase from Olsenella scatoligenes

Lu, Q., Wei, Y., Lin, L., Liu, J., Duan, Y., Li, Y., Zhai, W., Liu, Y., Ang, E.L., Zhao, H., Yuchi, Z., Zhang, Y.

(2021) ACS Catal 11: 5789-5794

DOI: https://doi.org/10.1021/acscatal.1c01253

Macromolecule Content

Total Structure Weight: 185.02 kDa
Atom Count: 11,337
Modelled Residue Count: 1,536
Deposited Residue Count: 1,616
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyphenylacetic acid decarboxylase	A, B	808	Tractidigestivibacter scatoligenes	Mutation(s): 0 Gene Names: AUL39_01475
UniProt
Find proteins for A0A100YWM3 (Tractidigestivibacter scatoligenes) Explore A0A100YWM3 Go to UniProtKB: A0A100YWM3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A100YWM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4HP (Subject of Investigation/LOI) Query on 4HP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	4-HYDROXYPHENYLACETATE C₈ H₈ O₃ XQXPVVBIMDBYFF-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: 3.53 Å
R-Value Free: 0.358
R-Value Work: 0.290
R-Value Observed: 0.295
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.946	α = 90
b = 225.548	β = 90
c = 234.679	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31870049

Revision History (Full details and data files)

Version 1.0: 2021-07-28
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.