7UOI

Crystallographic structure of DapE from Enterococcus faecium

• PDB DOI: https://doi.org/10.2210/pdb7UOI/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecium 1,231,410
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-04-12 Released: 2023-04-12 
• Deposition Author(s): Gonzalez-Segura, L., Diaz-Vilchis, A., Terrazas-Lopez, M., Diaz-Sanchez, A.G.
• Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT), Facultad de Quimica, Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.181 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Literature

Structural basis of Enterococcus faecium DapE enzyme interaction with potential bioactive molecules

Terrazas-Lopez, M., Gonzalez-Segura, L., Diaz-Vilchis, A., Lobo-Galo, N., Bustos-Jaimes, I., Martinez, A., Diaz-Sanchez, A.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.23 kDa 
• Atom Count: 3,699 
• Modelled Residue Count: 383 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
succinyl-diaminopimelate desuccinylase	A	402	Enterococcus faecium 1,231,410	Mutation(s): 0  Gene Names: EFTG_01132 EC: 3.5.1.18
UniProt
Find proteins for A0A1S8KJG1 (Enterococcus faecium) Explore A0A1S8KJG1  Go to UniProtKB:  A0A1S8KJG1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.181 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.486	α = 90
b = 45.378	β = 103.65
c = 78.751	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Gonzalez-Segura, L., Diaz-Vilchis, A., Terrazas-Lopez, M., Diaz-Sanchez, A.G.

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Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	PN-2015-587
Facultad de Quimica	Mexico	UNAM 5000-9129
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)	Mexico	IN227920

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2023-04-19
  Changes: Author supporting evidence