PDB-9ebf: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr...

ID or keywords:

Entry

Database: PDB / ID: 9ebf

Title

FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, borolane-based compound Q41 bound in crystal form 6

Components

Uncharacterized hydrolase SAUSA300_2518

Keywords

HYDROLASE / FphE / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / boron / serine-boron / histidine-boron

Function / homology

Hydrolases / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / membrane / : / Uncharacterized hydrolase SAUSA300_2518

Function and homology information

Biological species

Staphylococcus aureus subsp. aureus USA300 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Fellner, M.

Funding support

New Zealand, 1items

Citation

Journal: To Be Published
Title: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, borolane-based compound Q41 bound in crystal form 6
Authors: Fellner, M.

History

Deposition	Nov 12, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 21, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ebf.cif.gz	449.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9ebf.ent.gz	376 KB	Display	PDB format
PDBx/mmJSON format	9ebf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eb/9ebf ftp://data.pdbj.org/pub/pdb/validation_reports/eb/9ebf	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: Uncharacterized hydrolase SAUSA300_2518

B: Uncharacterized hydrolase SAUSA300_2518

C: Uncharacterized hydrolase SAUSA300_2518

D: Uncharacterized hydrolase SAUSA300_2518

hetero molecules

126 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized hydrolase SAUSA300_2518

B: Uncharacterized hydrolase SAUSA300_2518

hetero molecules

defined by author&software
Evidence: gel filtration
63.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Uncharacterized hydrolase SAUSA300_2518

D: Uncharacterized hydrolase SAUSA300_2518

hetero molecules

defined by author&software
63.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	212.286, 212.286, 212.286
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

#1: Protein	Uncharacterized hydrolase SAUSA300_2518 Mass: 31275.100 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria) Gene: SAUSA300_2518 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical	ChemComp-XPU / 2-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzene-1-sulfonamide Mass: 297.178 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₃H₂₀BNO₄S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.19 Å³/Da / Density % sol: 61.4 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 16 uL 11.2 mg/mL FphE (10 mM HEPES pH 7.5, 100 mM NaCl) were mixed with 6 uL Q41 (50 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-Q41 solution was mixed with 0.3 uL of reservoir ...Details: 16 uL 11.2 mg/mL FphE (10 mM HEPES pH 7.5, 100 mM NaCl) were mixed with 6 uL Q41 (50 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-Q41 solution was mixed with 0.3 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 180 mM Potassium Thiocyanate, 100 mM Sodium acetate pH 5.5, 22.5% PEG 2000 MME. Crystal was frozen in a solution of ~25% glycerol, 75% reservoir.

Crystal

Density Matthews: 3.19 Å³/Da / Density % sol: 61.4 %

Crystal grow

Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 16 uL 11.2 mg/mL FphE (10 mM HEPES pH 7.5, 100 mM NaCl) were mixed with 6 uL Q41 (50 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-Q41 solution was mixed with 0.3 uL of reservoir ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.954 Å / Relative weight: 1
Reflection	Resolution: 2.5→47.47 Å / Num. obs: 54846 / % possible obs: 99.9 % / Redundancy: 31.2 % / CC_1/2: 1 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.022 / R_rim(I) all: 0.124 / Χ²: 1.01 / Net I/σ(I): 23.7 / Num. measured all: 1710359
Reflection shell	Resolution: 2.5→2.57 Å / % possible obs: 98.4 % / Redundancy: 30.5 % / R_merge(I) obs: 2.179 / Num. measured all: 135026 / Num. unique obs: 4421 / CC_1/2: 0.692 / R_pim(I) all: 0.394 / R_rim(I) all: 2.215 / Χ²: 1 / Net I/σ(I) obs: 2.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→47.47 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2221	2769	5.05 %
R_work	0.1831	-	-
obs	0.185	54834	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→47.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8800	0	52	76	8928

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9064
X-RAY DIFFRACTION	f_angle_d	1.008	12308
X-RAY DIFFRACTION	f_dihedral_angle_d	16.973	3376
X-RAY DIFFRACTION	f_chiral_restr	0.057	1332
X-RAY DIFFRACTION	f_plane_restr	0.01	1612

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.54	0.3258	138	0.3084	2516	X-RAY DIFFRACTION	97
2.54-2.59	0.3498	136	0.2736	2632	X-RAY DIFFRACTION	100
2.59-2.64	0.2747	147	0.2653	2552	X-RAY DIFFRACTION	100
2.64-2.69	0.2404	123	0.2541	2584	X-RAY DIFFRACTION	100
2.69-2.75	0.3085	158	0.2507	2574	X-RAY DIFFRACTION	100
2.75-2.81	0.3145	119	0.2753	2601	X-RAY DIFFRACTION	100
2.82-2.89	0.2917	158	0.2702	2600	X-RAY DIFFRACTION	100
2.89-2.96	0.312	129	0.2528	2575	X-RAY DIFFRACTION	100
2.96-3.05	0.2825	168	0.2367	2551	X-RAY DIFFRACTION	100
3.05-3.15	0.2766	140	0.2214	2614	X-RAY DIFFRACTION	100
3.15-3.26	0.2944	131	0.2342	2591	X-RAY DIFFRACTION	100
3.26-3.39	0.2516	116	0.2187	2618	X-RAY DIFFRACTION	100
3.39-3.55	0.2547	136	0.2188	2602	X-RAY DIFFRACTION	100
3.55-3.73	0.2253	116	0.1821	2643	X-RAY DIFFRACTION	100
3.73-3.97	0.2284	171	0.1674	2559	X-RAY DIFFRACTION	100
3.97-4.27	0.1966	111	0.156	2646	X-RAY DIFFRACTION	100
4.27-4.7	0.1791	162	0.1422	2601	X-RAY DIFFRACTION	100
4.7-5.38	0.1931	144	0.1439	2619	X-RAY DIFFRACTION	100
5.39-6.77	0.1975	155	0.1725	2635	X-RAY DIFFRACTION	100
6.78-47.47	0.1446	111	0.1319	2752	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.6741	0.1588	0.5975	2.3181	-0.0245	2.6053	0.1321	-1.0867	0.6342	0.3272	-0.0002	0.0586	-0.6313	-0.0075	-0.1063	0.5329	-0.108	0.1254	0.6977	-0.2924	0.6142	10.6745	-17.561	-80.8968
2	3.7084	-0.8978	1.269	0.4654	-1.1781	2.3807	0.2229	-0.8482	0.198	-0.1243	0.0746	0.5967	0.0523	-0.5238	-0.3222	0.4219	-0.1215	0.0213	0.6555	-0.0689	0.5454	-0.1898	-29.5336	-88.4484
3	4.437	-1.6031	2.0429	3.956	-1.058	3.799	0.3795	-0.352	-0.4974	-0.1164	0.0869	0.2499	0.5038	-0.3275	-0.4423	0.5981	-0.2497	-0.1057	0.8079	0.1199	0.4827	18.7095	-50.6548	-75.0095
4	1.2341	-0.337	0.0908	1.7887	-0.341	2.5036	0.314	-0.1592	-0.2182	0.4512	-0.1284	-0.5386	0.5259	0.5194	-0.2063	0.6808	-0.1247	-0.3044	0.833	0.1266	0.8119	34.8174	-61.1804	-61.1253
5	2.0568	-0.5484	0.3731	1.7294	-0.2143	2.5414	0.2991	-0.4093	0.0274	0.4696	-0.0995	-0.1596	0.1216	0.2239	-0.2277	0.6241	-0.2622	-0.1443	0.8227	0.0537	0.5695	30.1744	-47.5533	-56.5513
6	4.295	-3.8531	3.0086	4.2332	-2.119	1.9233	0.5781	-0.1169	-0.0236	-0.3754	-0.4983	-0.0957	0.2717	0.2783	-0.0616	0.5188	-0.1692	-0.012	0.6313	0.0499	0.4524	22.3385	-41.1192	-85.8205
7	6.2489	0.8552	0.7427	1.1729	-0.1635	3.4554	0.1543	-0.4427	0.7961	-0.194	-0.0165	0.2037	-0.4144	-0.1593	-0.1432	0.4676	-0.0125	0.0779	0.3268	-0.0768	0.5065	2.2679	-20.9149	-95.5293
8	5.4378	-0.2346	-0.276	2.9755	0.5239	3.4238	0.6388	-1.5855	0.2325	0.48	-0.6673	-0.1838	-0.043	0.4382	0.0941	0.5841	-0.3366	0.0981	0.992	-0.1436	0.4836	58.2021	-17.6144	-87.1087
9	1.6525	0.453	-1.5497	3.8755	0.545	1.715	0.7101	-1.6158	1.1165	0.4475	-0.5736	0.4663	-0.3329	0.3922	-0.0303	0.6921	-0.3847	0.2429	1.12	-0.4821	0.7671	45.9141	-13.3723	-84.1297
10	3.7102	-1.1724	-0.4293	8.2471	0.5265	3.4069	0.0768	-0.1331	-0.1976	-0.012	-0.2188	0.6625	0.2372	0.1552	0.144	0.4577	-0.1117	0.0311	0.5011	0.0393	0.4485	42.0613	-43.9395	-98.0877
11	3.4017	1.1394	0.0839	4.4974	0.2514	4.1359	-0.0753	-0.0002	-0.8306	-0.7175	0.0295	-0.5519	1.0454	0.3945	0.0553	0.7202	0.073	0.065	0.4598	0.0098	0.6924	51.1615	-65.8122	-102.0702
12	2.1529	0.7019	-0.6787	3.6091	-0.3209	3.3923	0.0757	-0.3806	-0.4768	-0.1129	-0.2163	-0.9068	0.3046	0.8043	0.1061	0.4068	0.034	0.0205	0.6214	0.0846	0.6882	57.1476	-56.5465	-93.6759
13	4.9589	0.3824	0.0035	7.7544	0.1115	2.0307	0.1328	-0.0782	0.2528	-0.7867	-0.1446	-0.0741	-0.1348	0.1682	-0.0088	0.5346	-0.1517	0.0676	0.4713	-0.0207	0.3656	46.6338	-26.25	-101.3945
14	2.4859	-0.5462	0.7371	2.6164	1.0926	1.2142	0.5638	-1.1207	1.7496	0.0054	-0.4667	0.8101	-0.5845	0.052	-0.0935	0.8008	-0.2868	0.3043	0.7805	-0.4716	1.2222	44.4225	-5.0174	-90.9682

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 115 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 116 through 152 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 153 through 200 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 201 through 276 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 136 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 137 through 200 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 201 through 276 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 75 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 76 through 152 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 153 through 200 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 201 through 276 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 152 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 153 through 200 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 201 through 276 )

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