PDB-8t88: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr...

ID or keywords:

Entry

Database: PDB / ID: 8t88

Title

FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone JJ004 bound

Components

Fluorophosphonate-binding serine hydrolase E

Keywords

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

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 USA300-0114 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.54 Å

Authors

Fellner, M.

Funding support

New Zealand, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2024
Title: Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections.
Authors: Jo, J. / Upadhyay, T. / Woods, E.C. / Park, K.W. / Pedowitz, N.J. / Jaworek-Korjakowska, J. / Wang, S. / Valdez, T.A. / Fellner, M. / Bogyo, M.

History

Deposition	Jun 22, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 6, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8t88.cif.gz	342.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8t88.ent.gz	284.3 KB	Display	PDB format
PDBx/mmJSON format	8t88.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8t88_validation.pdf.gz	891.3 KB	Display	wwPDB validaton report
Full document	8t88_full_validation.pdf.gz	895 KB	Display
Data in XML	8t88_validation.xml.gz	26.8 KB	Display
Data in CIF	8t88_validation.cif.gz	39.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t8/8t88 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/8t88	HTTPS FTP

-
Related structure data

Related structure data	8t87C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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: Fluorophosphonate-binding serine hydrolase E

B: Fluorophosphonate-binding serine hydrolase E

hetero molecules

63.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	46.743, 74.271, 73.638
Angle α, β, γ (deg.)	90.00, 91.70, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fluorophosphonate-binding serine hydrolase E Mass: 31275.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA300-0114 (bacteria) Gene: SAUSA300_2518 / Plasmid: F1010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical	ChemComp-YW0 / methyl 2-formyl-2-[4-(undec-10-ynamido)phenyl]hydrazine-1-carboxylate Mass: 373.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₇N₃O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.78 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 13 uL 19 mg/mL FphE (10 mM HEPES pH 7.5, 10 0mM NaCl) were mixed with 5 uL JJ004 (10 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-JJ004 solution was mixed with 0.2 uL of ...Details: 13 uL 19 mg/mL FphE (10 mM HEPES pH 7.5, 10 0mM NaCl) were mixed with 5 uL JJ004 (10 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-JJ004 solution was mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 0.18 M Magnesium chloride, 0.1 M Tris pH 8.5, 22.5 % w/v Polyethylene glycol monomethyl ether 2000. Crystal was frozen in a solution of ~25% glycerol, 75% reservoir.

Crystal

Density Matthews: 2.04 Å³/Da / Density % sol: 39.78 %

Crystal grow

Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 13 uL 19 mg/mL FphE (10 mM HEPES pH 7.5, 10 0mM NaCl) were mixed with 5 uL JJ004 (10 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-JJ004 solution was mixed with 0.2 uL of ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.54→39.99 Å / Num. obs: 73321 / % possible obs: 98 % / Redundancy: 5.3 % / CC_1/2: 1 / R_merge(I) obs: 0.037 / R_pim(I) all: 0.018 / R_rim(I) all: 0.041 / Χ²: 0.65 / Net I/σ(I): 17.5 / Num. measured all: 390181
Reflection shell	Resolution: 1.54→1.56 Å / % possible obs: 95.1 % / Redundancy: 5.2 % / R_merge(I) obs: 1.051 / Num. measured all: 18405 / Num. unique obs: 3543 / CC_1/2: 0.598 / R_pim(I) all: 0.498 / R_rim(I) all: 1.166 / Χ²: 0.62 / Net I/σ(I) obs: 1.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless	0.7.8	data scaling
XDS		data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.54→39.99 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1846	3528	4.81 %
R_work	0.1565	-	-
obs	0.1579	73279	97.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.54→39.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4386	0	56	458	4900

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4693
X-RAY DIFFRACTION	f_angle_d	1.077	6386
X-RAY DIFFRACTION	f_dihedral_angle_d	9.573	659
X-RAY DIFFRACTION	f_chiral_restr	0.059	681
X-RAY DIFFRACTION	f_plane_restr	0.017	851

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 (%)
1.54-1.56	0.3162	127	0.3074	2718	X-RAY DIFFRACTION	95
1.56-1.58	0.289	133	0.2561	2743	X-RAY DIFFRACTION	97
1.58-1.6	0.2591	147	0.2275	2765	X-RAY DIFFRACTION	97
1.6-1.63	0.2833	112	0.2161	2789	X-RAY DIFFRACTION	97
1.63-1.65	0.2623	139	0.2083	2768	X-RAY DIFFRACTION	97
1.65-1.68	0.2452	159	0.2049	2751	X-RAY DIFFRACTION	97
1.68-1.71	0.2177	130	0.1935	2773	X-RAY DIFFRACTION	98
1.71-1.75	0.2315	133	0.1946	2772	X-RAY DIFFRACTION	98
1.75-1.78	0.2091	132	0.1881	2799	X-RAY DIFFRACTION	98
1.78-1.82	0.2122	131	0.1869	2780	X-RAY DIFFRACTION	98
1.82-1.86	0.2109	129	0.1845	2851	X-RAY DIFFRACTION	98
1.86-1.91	0.2193	156	0.1823	2732	X-RAY DIFFRACTION	98
1.91-1.96	0.1947	168	0.167	2767	X-RAY DIFFRACTION	98
1.96-2.02	0.1949	148	0.1599	2671	X-RAY DIFFRACTION	94
2.02-2.08	0.1865	144	0.1565	2766	X-RAY DIFFRACTION	97
2.08-2.16	0.1866	158	0.1568	2794	X-RAY DIFFRACTION	99
2.16-2.25	0.1637	143	0.1526	2828	X-RAY DIFFRACTION	99
2.25-2.35	0.1942	151	0.1434	2811	X-RAY DIFFRACTION	99
2.35-2.47	0.1935	169	0.1483	2821	X-RAY DIFFRACTION	99
2.47-2.63	0.194	151	0.1554	2816	X-RAY DIFFRACTION	99
2.63-2.83	0.2091	112	0.16	2866	X-RAY DIFFRACTION	99
2.83-3.11	0.1838	146	0.1559	2825	X-RAY DIFFRACTION	99
3.11-3.56	0.1427	123	0.1521	2841	X-RAY DIFFRACTION	98
3.56-4.49	0.1524	112	0.1189	2789	X-RAY DIFFRACTION	96
4.49-39.99	0.1634	175	0.1454	2915	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	1.1205	0.1409	0.3464	1.0673	-0.0123	1.1589	-0.023	0.018	0.1932	-0.0145	0.0092	-0.0003	-0.1133	0.0199	0.0291	0.1222	0.013	0.019	0.1173	0.009	0.1619	-4.0554	-10.8961	7.509
2	1.3514	0.4725	0.3669	1.4545	0.6336	2.9647	0.0778	0.0278	-0.2249	-0.0236	-0.0454	-0.0126	0.2666	0.1248	-0.0053	0.1612	0.0319	-0.0013	0.1357	-0.0199	0.1965	-32.0298	-15.2431	-24.2599
3	2.4451	-0.1544	0.8007	1.4384	-0.2935	3.3971	0.103	0.2084	0.0251	-0.1323	0.1084	-0.2731	-0.0003	0.7373	-0.1999	0.1529	-0.0178	0.0399	0.319	-0.0577	0.207	-16.4134	-7.6166	-30.1004
4	1.3113	0.2698	1.4746	2.1636	-1.9104	4.262	0.2027	0.3247	-0.0914	-0.2946	-0.0117	-0.0959	0.3048	0.5622	-0.1576	0.2131	0.0755	0.0155	0.3221	-0.0723	0.1998	-20.8072	-15.3937	-36.8451
5	3.2398	0.0535	-0.6829	2.5544	0.0677	4.0931	0.029	-0.1032	0.3385	-0.0028	0.1703	-0.1765	-0.3641	0.4566	-0.1302	0.1745	-0.0537	0.0093	0.194	-0.0523	0.2047	-20.0237	-1.6332	-20.8848
6	2.5291	0.3786	-1.1837	1.9653	-0.1805	4.425	0.0381	0.1206	0.0673	-0.181	-0.015	0.0218	-0.1861	-0.0297	-0.0116	0.1668	0.0141	-0.0164	0.146	-0.0157	0.1568	-33.0785	-5.3693	-26.3189
7	9.5554	-3.5366	8.0484	1.9316	-1.8791	8.8226	-0.0229	-0.5522	-0.0858	0.0043	-0.0335	0.0418	0.577	-0.4622	-0.0086	0.3	-0.0315	0.0635	0.2709	0.0096	0.2168	-35.5635	-13.8624	-6.0344
8	5.0071	-2.711	6.9477	2.0534	-4.0815	9.86	0.1292	-0.2422	-0.0734	-0.1729	0.114	0.3391	0.2392	-0.6099	-0.2239	0.2202	-0.0275	0.0201	0.3206	-0.034	0.2774	-22.2628	-21.4251	9.5409
9	3.4144	-0.702	1.9029	4.0053	-4.0546	8.1892	-0.2141	-0.1422	0.2884	0.1815	0.0882	0.4979	-0.5632	-1.0097	0.1268	0.2322	0.0611	0.021	0.4208	-0.0739	0.3017	-20.6248	-13.3749	16.8393
10	8.4451	-5.6768	-2.9021	7.7097	1.9935	6.4517	-0.0301	-0.4378	0.181	-0.2323	-0.0437	0.5469	-0.706	-0.4655	0.0852	0.2072	0.0327	-0.0383	0.2532	-0.0212	0.2598	-18.5903	-10.3967	2.7664
11	1.3374	0.7147	2.8201	2.7284	2.1404	6.5357	0.133	0.1713	-0.2662	0.259	0.1792	-0.3368	0.4071	0.6423	-0.2726	0.1567	0.0324	0.013	0.1986	0.0116	0.1933	4.1731	-20.7296	11.4599
12	2.6843	0.1744	0.3711	2.7311	0.5825	2.1995	0.0327	-0.3098	0.1281	0.5022	-0.0454	0.0544	0.0708	-0.1693	0.0096	0.2345	0.009	0.0214	0.2015	-0.0217	0.1196	-4.1871	-15.3288	24.9737

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 166 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 167 through 276 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 0 through 31 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 32 through 51 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 52 through 96 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 97 through 136 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 137 through 152 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 153 through 166 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 167 through 183 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 184 through 200 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 201 through 221 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 222 through 276 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi