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

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10378
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VQ5 (Subject of Investigation/LOI) Query on VQ5 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] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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		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: 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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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.