8K5T

The structure of EntE with2-methyl-3-chloro-benzoic acid sulfamoyl adenosine

• PDB DOI: https://doi.org/10.2210/pdb8K5T/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-07-24 Released: 2024-07-31 
• Deposition Author(s): Miyanaga, A., Ishikawa, F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.246 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Reprogrammed aryl acid adenylation domain with an enlarged substrate binding pocket

Ishikawa, F., Miyanaga, A., Kudo, F., Eguchi, T., Tanabe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 123.66 kDa 
• Atom Count: 8,263 
• Modelled Residue Count: 1,045 
• Deposited Residue Count: 1,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterobactin synthase component E	A, B	556	Escherichia coli	Mutation(s): 1  Gene Names: entE, b0594, JW0586 EC: 6.3.2.14 (PDB Primary Data), 6.2.1.71 (PDB Primary Data)
UniProt
Find proteins for P10378 (Escherichia coli (strain K12)) Explore P10378  Go to UniProtKB:  P10378

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VQ5 (Subject of Investigation/LOI)	C [auth A], D [auth B]	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-(3-chloranyl-2-methyl-phenyl)carbonylsulfamate C18 H19 Cl N6 O7 S NHHJUHWTWOXCDU-XWXWGSFUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.246 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.971	α = 90
b = 56.866	β = 96.44
c = 171.888	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Miyanaga, A., Ishikawa, F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release