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
Modeled 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

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.