9COM | pdb_00009com

FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, unbound dimer crystal form 5

PDB DOI: https://doi.org/10.2210/pdb9COM/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus USA300
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-17 Released: 2025-08-06
Deposition Author(s): Fellner, M.
Funding Organization(s): Capability Build Funding - New Zealand Synchrotron Group Ltd

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

FphE, Staphylococcus aureus, S. aureus, fluorophosphonate-binding, serine hydrolases, lipase

Fellner, M.

To be published.

Macromolecule Content

Total Structure Weight: 93.86 kDa
Atom Count: 6,800
Modeled Residue Count: 833
Deposited Residue Count: 837
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FphE	A, B, C	279	Staphylococcus aureus subsp. aureus USA300	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
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.248 (Depositor), 0.248 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.399	α = 90
b = 86.797	β = 90
c = 137.764	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-06

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: 2025-08-06
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.