8G49 | pdb_00008g49

FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone compound 3 bound

PDB DOI: https://doi.org/10.2210/pdb8G49/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus USA300-CA-263
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-08 Released: 2024-02-21
Deposition Author(s): Fellner, M., Bakker, A.T., Martin, N.I., Stelt, M.
Funding Organization(s): Capability Build Funding - New Zealand Synchrotron Group Ltd

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.198 (Depositor), 0.190 (DCC)
R-Value Work:
0.175 (Depositor), 0.170 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone compound 3 bound

Fellner, M., Bakker, A.T., Martin, N.I., Stelt, M.

To be published.

Macromolecule Content

Total Structure Weight: 31.69 kDa
Atom Count: 2,427
Modelled Residue Count: 276
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorophosphonate-binding serine hydrolase E	A	279	Staphylococcus aureus USA300-CA-263	Mutation(s): 0 Gene Names: SAUSA300_2518 EC: 3
UniProt
Find proteins for Q2FDS6 (Staphylococcus aureus (strain USA300)) Explore Q2FDS6 Go to UniProtKB: Q2FDS6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FDS6
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YKF (Subject of Investigation/LOI) Query on YKF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	methyl 2-formyl-2-[3-methyl-4-(3-phenoxybenzamido)phenyl]hydrazine-1-carboxylate C₂₃ H₂₁ N₃ O₅ IFPAECUTANEMNN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.198 (Depositor), 0.190 (DCC)
R-Value Work: 0.175 (Depositor), 0.170 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.434	α = 90
b = 46.434	β = 90
c = 218.372	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Capability Build Funding - New Zealand Synchrotron Group Ltd	New Zealand	--

Revision History (Full details and data files)

Version 1.0: 2024-02-21
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary

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.