PDB-9s75: Extracellular serine protease Jep from mouse-adapted S. aureus st...

ID or keywords:

Entry

Database: PDB / ID: 9s75

Title

Extracellular serine protease Jep from mouse-adapted S. aureus strain JSNZ in complex with inhibitor AEBSF

Components

JSNZ extracellular serine protease Jep

Keywords

HYDROLASE / serine protease / trypsin-like / beta-barrel / proteolysis / virulence

Function / homology

4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / BETA-MERCAPTOETHANOL / IODIDE ION

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Schmoeker, O. / Peringathara, S. / Wolfgramm, H. / Bludau, E. / Girbardt, B. / Palm, G.J. / Hoppen, J. / Holtfreter, S. / Lammers, M.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Biochemical and Structural Characterization of novel extracellular serine protease Jep from mouse-adapted S. aureus strain JSNZ
Authors: Peringathara, S. / Schmoeker, O. / Bludau, E. / Wolfgramm, H. / Girbardt, B. / Palm, G.J. / Hoppen, J. / Lammers, M. / Holtfreter, S.

History

Deposition	Aug 2, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 12, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9s75.cif.gz	947.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9s75.ent.gz	652.8 KB	Display	PDB format
PDBx/mmJSON format	9s75.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/s7/9s75 ftp://data.pdbj.org/pub/pdb/validation_reports/s7/9s75	HTTPS FTP

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Related structure data

Related structure data	9s74C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: JSNZ extracellular serine protease Jep

B: JSNZ extracellular serine protease Jep

C: JSNZ extracellular serine protease Jep

D: JSNZ extracellular serine protease Jep

E: JSNZ extracellular serine protease Jep

hetero molecules

123 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: JSNZ extracellular serine protease Jep

hetero molecules

defined by author
Evidence: gel filtration
24.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: JSNZ extracellular serine protease Jep

hetero molecules

defined by author
Evidence: gel filtration
24.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: JSNZ extracellular serine protease Jep

hetero molecules

defined by author
Evidence: gel filtration
24.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: JSNZ extracellular serine protease Jep

hetero molecules

defined by author
Evidence: gel filtration
24.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: JSNZ extracellular serine protease Jep

hetero molecules

defined by author
Evidence: gel filtration
24.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	272.143, 49.508, 67.304
Angle α, β, γ (deg.)	90, 96.043, 90
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	E-307- IOD
2	1	E-441- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 204 / Label seq-ID: 1 - 204

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20

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Protein , 1 types, 5 molecules ABCDE

#1: Protein	JSNZ extracellular serine protease Jep Mass: 23201.006 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: The crystallization construct corresponds to the mature protease without N-terminal 35aa signal peptide. The construct carries a C-terminal Strep-tag as expression tag (not resolved). Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: JSNZ CC88 / Plasmid: pTripleTREP / Details (production host): doi: 10.1186/s12934-025-02736-7 Production host: Staphylococcus aureus subsp. aureus RN4220 (bacteria) References: glutamyl endopeptidase

#1: Protein

JSNZ extracellular serine protease Jep

Mass: 23201.006 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: The crystallization construct corresponds to the mature protease without N-terminal 35aa signal peptide. The construct carries a C-terminal Strep-tag as expression tag (not resolved).
Source: (gene. exp.)

Staphylococcus aureus (bacteria) / Strain: JSNZ CC88 / Plasmid: pTripleTREP / Details (production host): doi: 10.1186/s12934-025-02736-7
Production host:

Staphylococcus aureus subsp. aureus RN4220 (bacteria)
References: glutamyl endopeptidase

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Non-polymers , 6 types, 496 molecules

#2: Chemical	ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF Mass: 203.234 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₀FNO₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: I
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.09 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15M ammonium iodide, 20% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 1.8 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2025

Radiation

Monochromator: SILICON111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.8 Å / Relative weight: 1

Reflection

Resolution: 1.8→45.26 Å / Num. obs: 78159 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / B_iso Wilson estimate: 16.44 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.051 / R_rim(I) all: 0.093 / R_sym value: 0.077 / Χ²: 0.76 / Net I/σ(I): 10.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	R_sym value	Χ²	% possible all
9.18-45.26	6.7	16	680	0.997	0.034	0.066	0.057	0.83	98.6
1.8-1.84	3.1	2.5	2396	0.627	0.279	0.416	0.307	0.3	50.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
Coot	0.9.8.95	model building
PHASER	2.8.3	phasing
XDS	BUILT 20230630	data scaling
XDS	BUILT 20230630	data reduction
MxCuBE		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→45.26 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.942 / SU B: 11.003 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2616	3876	4.959 %
R_work	0.2195	74282	-
all	0.222	-	-
obs	-	78158	93.916 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.753 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.154 Å²	-0 Å²	0.285 Å²
2-	-	-1.963 Å²	0 Å²
3-	-	-	0.732 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→45.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7745	0	123	439	8307

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	8005
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7591
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.019	0.1	113183
X-RAY DIFFRACTION	r_angle_refined_deg	1.928	1.798	10861
X-RAY DIFFRACTION	r_angle_other_deg	0.655	1.761	17545
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.918	5	1033
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.762	5	25
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.133	10	1350
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.262	10	336
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	1224
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	9357
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1729
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	1331
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	7256
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	4000
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	4375
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	326
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.112	0.2	6
X-RAY DIFFRACTION	r_metal_ion_refined	0.126	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.327	0.2	49
X-RAY DIFFRACTION	r_nbd_other	0.282	0.2	160
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.454	0.2	17
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.397	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.223	0.781	4089
X-RAY DIFFRACTION	r_mcbond_other	2.222	0.781	4090
X-RAY DIFFRACTION	r_mcangle_it	3.5	1.401	5108
X-RAY DIFFRACTION	r_mcangle_other	3.5	1.402	5109
X-RAY DIFFRACTION	r_scbond_it	2.754	0.918	3916
X-RAY DIFFRACTION	r_scbond_other	2.753	0.918	3917
X-RAY DIFFRACTION	r_scangle_it	4.179	1.639	5744
X-RAY DIFFRACTION	r_scangle_other	4.178	1.639	5745
X-RAY DIFFRACTION	r_lrange_it	7.272	17.617	115556
X-RAY DIFFRACTION	r_lrange_other	7.226	17.608	115508
X-RAY DIFFRACTION	r_rigid_bond_restr	4.265	3	15596
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.06	0.05	6550
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.056	0.05	6594
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.066	0.05	6518
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.058	0.05	6556
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.045	0.05	6574
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.062	0.05	6504
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.062	0.05	6506
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.066	0.05	6526
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.059	0.05	6547
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.06	0.05	6545

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06038	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.06038	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05573	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.05573	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06608	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.06608	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.05831	0.0501
4	8	E	X-RAY DIFFRACTION	Local ncs	0.05831	0.0501
5	9	B	X-RAY DIFFRACTION	Local ncs	0.04513	0.0501
5	10	C	X-RAY DIFFRACTION	Local ncs	0.04513	0.0501
6	11	B	X-RAY DIFFRACTION	Local ncs	0.06246	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.06246	0.0501
7	13	B	X-RAY DIFFRACTION	Local ncs	0.06242	0.0501
7	14	E	X-RAY DIFFRACTION	Local ncs	0.06242	0.0501
8	15	C	X-RAY DIFFRACTION	Local ncs	0.0657	0.0501
8	16	D	X-RAY DIFFRACTION	Local ncs	0.0657	0.0501
9	17	C	X-RAY DIFFRACTION	Local ncs	0.05944	0.0501
9	18	E	X-RAY DIFFRACTION	Local ncs	0.05944	0.0501
10	19	D	X-RAY DIFFRACTION	Local ncs	0.06049	0.0501
10	20	E	X-RAY DIFFRACTION	Local ncs	0.06049	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.8-1.847	0.356	163	0.363	3046	0.362	6155	0.848	0.889	52.1365	0.329
1.847-1.897	0.37	206	0.309	4068	0.312	5947	0.903	0.94	71.8682	0.289
1.897-1.952	0.294	280	0.26	5156	0.261	5739	0.939	0.957	94.7203	0.242
1.952-2.012	0.285	284	0.238	5310	0.241	5599	0.951	0.966	99.9107	0.226
2.012-2.078	0.277	267	0.228	5213	0.23	5495	0.958	0.969	99.727	0.216
2.078-2.151	0.265	252	0.208	5024	0.21	5282	0.959	0.976	99.8864	0.201
2.151-2.232	0.289	259	0.209	4816	0.213	5082	0.948	0.974	99.8623	0.203
2.232-2.323	0.274	220	0.212	4676	0.215	4912	0.952	0.975	99.6743	0.21
2.323-2.426	0.243	210	0.196	4471	0.198	4689	0.966	0.979	99.8294	0.198
2.426-2.544	0.274	222	0.199	4294	0.202	4521	0.957	0.978	99.8894	0.203
2.544-2.681	0.268	209	0.217	4084	0.22	4299	0.959	0.975	99.8604	0.229
2.681-2.843	0.265	213	0.211	3794	0.213	4026	0.956	0.976	99.5281	0.227
2.843-3.038	0.239	213	0.21	3632	0.211	3850	0.969	0.977	99.8701	0.239
3.038-3.28	0.239	162	0.208	3415	0.209	3581	0.969	0.98	99.8883	0.242
3.28-3.592	0.253	160	0.215	3127	0.217	3293	0.973	0.98	99.8178	0.257
3.592-4.012	0.249	149	0.2	2832	0.202	2995	0.973	0.982	99.5326	0.25
4.012-4.627	0.208	147	0.187	2500	0.189	2652	0.982	0.985	99.8115	0.255
4.627-5.652	0.237	119	0.212	2142	0.213	2267	0.983	0.985	99.7353	0.277
5.652-7.932	0.244	81	0.254	1682	0.254	1765	0.976	0.979	99.8867	0.331
7.932-45.26	0.334	60	0.299	1000	0.302	1065	0.975	0.972	99.5305	0.443

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	1.8487	-0.9014	-0.5678	4.2548	0.3159	3.2209	0.1797	0.0736	0.0927	-0.4484	0.1545	-0.6652	0.0638	0.2749	-0.3342	0.1276	0.0265	0.1484	0.1012	-0.027	0.2563	63.9306	-1.2864	15.8807
2	1.4065	-0.4523	-0.6716	4.8492	-0.3238	3.3091	0.1056	-0.0422	-0.0877	-0.0438	-0.1195	-0.2726	0.0128	0.0247	0.0139	0.0385	0.0436	0.0375	0.0796	0.0828	0.0944	38.8244	-25.0775	2.9944
3	1.6264	0.6973	-0.641	3.3355	0.426	4.1627	0.016	-0.0255	-0.122	-0.0841	-0.0119	-0.0465	0.1841	-0.6847	-0.0041	0.0222	-0.0663	-0.0002	0.3365	0.0168	0.0162	12.9806	-25.4796	23.7811
4	1.3793	0.3214	-0.4388	4.8539	0.9734	2.7502	-0.0088	0.0067	-0.0637	0.3335	0.0801	0.4308	0.1217	-0.1446	-0.0713	0.0731	0.0522	0.0744	0.0707	0.0726	0.1076	39.1625	-0.3925	38.0264
5	2.0218	0.2562	-0.508	3.8662	-0.0837	3.8041	-0.0444	0.2653	0.0259	0.131	0.1634	-0.1214	0.435	0.4666	-0.119	0.0687	0.1009	-0.0039	0.2341	0.0239	0.0222	12.1209	-0.6137	-11.3247

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 301
2	X-RAY DIFFRACTION	2	ALL	B	1 - 301
3	X-RAY DIFFRACTION	3	ALL	C	1 - 302
4	X-RAY DIFFRACTION	4	ALL	D	1 - 301
5	X-RAY DIFFRACTION	5	ALL	E	1 - 302

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Protein , 1 types, 5 molecules ABCDE

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Non-polymers , 6 types, 496 molecules

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