5EGN | pdb_00005egn

Est816 as an N-Acyl homoserine lactone degrading enzyme

PDB DOI: https://doi.org/10.2210/pdb5EGN/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-10-27 Released: 2016-11-02
Deposition Author(s): Xie, W., Liu, X., Cao, L., Liu, Y.
Funding Organization(s): Guangdong Innovative Research Team Program, The Fundamental Research Funds for the Central Universities, National Sciences Foundation of China, Science and Technology Program of Guangzhou

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.264 (Depositor), 0.266 (DCC)
R-Value Work:
0.219 (Depositor), 0.223 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5EGN

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

Literature

Est816 as an N-Acyl homoserine lactone degrading enzyme

Xie, W., Liu, X., Cao, L., Liu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 236.31 kDa
Atom Count: 16,184
Modeled Residue Count: 2,074
Deposited Residue Count: 2,168
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B, C, D, E A, B, C, D, E, F, G, H	271	uncultured bacterium	Mutation(s): 2 Gene Names: est816 EC: 3.1.1.1
UniProt
Find proteins for A0ACD6B8M3 (uncultured bacterium) Explore A0ACD6B8M3 Go to UniProtKB: A0ACD6B8M3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8M3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.264 (Depositor), 0.266 (DCC)
R-Value Work: 0.219 (Depositor), 0.223 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.806	α = 90
b = 78.545	β = 99.37
c = 116.472	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Guangdong Innovative Research Team Program	China	2011Y038
The Fundamental Research Funds for the Central Universities	China	15lgjc02
National Sciences Foundation of China	China	31100579
Science and Technology Program of Guangzhou	China	201504010025

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.