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- PDB-9s74: Extracellular serine protease Jep from mouse-adapted S. aureus st... -

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Basic information

Entry
Database: PDB / ID: 9s74
TitleExtracellular serine protease Jep from mouse-adapted S. aureus strain JSNZ
ComponentsJSNZ extracellular serine protease Jep
KeywordsHYDROLASE / serine protease / trypsin-like / beta-barrel / proteolysis / virulence
Function / homology:
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsSchmoeker, O. / Peringathara, S. / Wolfgramm, H. / Bludau, E. / Girbardt, B. / Palm, G.J. / Hoppen, J. / Holtfreter, S. / Lammers, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)443535983 Germany
CitationJournal: 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
DepositionAug 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JSNZ extracellular serine protease Jep
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3754
Polymers23,2011
Non-polymers1743
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.261, 49.488, 68.383
Angle α, β, γ (deg.)90, 113.324, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

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Components

#1: Protein JSNZ extracellular serine protease Jep


Mass: 23201.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct corresponds to the the mature protease without N-terminal 35aa signal peptide. Amino acids N59, N60, R61, H62 are not resolved in the crystal structure. The construct carries a ...Details: The construct corresponds to the the mature protease without N-terminal 35aa signal peptide. Amino acids N59, N60, R61, H62 are not resolved in the crystal structure. 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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 0.2M potassium sulfate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.72932 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2024
RadiationMonochromator: SILICON111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 0.98→29.62 Å / Num. obs: 101075 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 9.65 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.055 / Rrim(I) all: 0.106 / Rsym value: 0.09 / Χ2: 0.97 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
5.37-36.616.66560.9850.050.0940.0791.0198.6
0.98-16.948640.7550.6151.1660.9870.9395.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Coot0.9.8.95model building
PHASER2.8.3phasing
XDSBUILT 20230630data scaling
XDSBUILT 20230630data reduction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→29.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.712 / SU ML: 0.017 / Cross valid method: FREE R-VALUE / ESU R: 0.022 / ESU R Free: 0.022
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1625 5213 5.158 %
Rwork0.1476 95861 -
all0.148 --
obs-101074 97.204 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.481 Å2
Baniso -1Baniso -2Baniso -3
1-0.381 Å2-0 Å20.58 Å2
2---0.486 Å2-0 Å2
3----0.288 Å2
Refinement stepCycle: LAST / Resolution: 0.98→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 7 247 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121575
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161515
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.8042144
X-RAY DIFFRACTIONr_angle_other_deg0.6551.7573505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.42554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00110272
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.1581063
X-RAY DIFFRACTIONr_chiral_restr0.1050.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02330
X-RAY DIFFRACTIONr_nbd_refined0.2580.2245
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21378
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2779
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.7710.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4350.217
X-RAY DIFFRACTIONr_nbd_other0.3580.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.235
X-RAY DIFFRACTIONr_mcbond_it4.141.364810
X-RAY DIFFRACTIONr_mcbond_other4.1291.364810
X-RAY DIFFRACTIONr_mcangle_it5.9472.4581012
X-RAY DIFFRACTIONr_mcangle_other5.9552.461013
X-RAY DIFFRACTIONr_scbond_it5.5861.644765
X-RAY DIFFRACTIONr_scbond_other5.511.628762
X-RAY DIFFRACTIONr_scangle_it7.8582.9081126
X-RAY DIFFRACTIONr_scangle_other7.772.8741121
X-RAY DIFFRACTIONr_lrange_it15.4519.4861764
X-RAY DIFFRACTIONr_lrange_other13.67916.4351693
X-RAY DIFFRACTIONr_rigid_bond_restr3.79933090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-1.0050.2693720.2516922X-RAY DIFFRACTION95.4088
1.005-1.0330.213520.2246679X-RAY DIFFRACTION94.4773
1.033-1.0630.2023860.1776575X-RAY DIFFRACTION96.173
1.063-1.0960.1763350.1516486X-RAY DIFFRACTION96.3146
1.096-1.1310.1273320.1326262X-RAY DIFFRACTION96.6012
1.131-1.1710.1363500.1216060X-RAY DIFFRACTION96.8132
1.171-1.2150.133090.1175913X-RAY DIFFRACTION97.3557
1.215-1.2650.1432890.1195707X-RAY DIFFRACTION97.4009
1.265-1.3210.1382590.1215487X-RAY DIFFRACTION97.5386
1.321-1.3850.1282680.1195177X-RAY DIFFRACTION96.1844
1.385-1.460.1422870.1194960X-RAY DIFFRACTION98.0381
1.46-1.5480.1392890.1144729X-RAY DIFFRACTION98.6436
1.548-1.6550.1472220.124497X-RAY DIFFRACTION98.7859
1.655-1.7870.1442360.1254159X-RAY DIFFRACTION99.1204
1.787-1.9570.1452490.1333835X-RAY DIFFRACTION99.0781
1.957-2.1870.1742010.143482X-RAY DIFFRACTION99.2455
2.187-2.5230.1561890.1473046X-RAY DIFFRACTION98.0898
2.523-3.0840.1741390.1712601X-RAY DIFFRACTION97.8921
3.084-4.3380.191940.1572092X-RAY DIFFRACTION100
4.338-29.620.206550.2211192X-RAY DIFFRACTION99.1256

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