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- PDB-9grg: StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine se... -

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Basic information

Entry
Database: PDB / ID: 9grg
TitleStmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with PMSF
ComponentsAlkaline serine protease
KeywordsHYDROLASE / alkaline serine protease / native / excreted protease / subtilisin-like
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase MprA-like catalytic domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / : / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. ...Peptidase MprA-like catalytic domain / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / : / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family
Similarity search - Domain/homology
phenylmethanesulfonic acid / Alkaline serine protease
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSommer, M. / Outzen, L. / Negm, A. / Windhorst, S. / Weber, W. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Sci Rep / Year: 2025
Title: Unveiling the structure, function and dynamics of StmPr1 in Stenotrophomonas maltophilia virulence.
Authors: Sommer, M. / Negm, A. / Outzen, L. / Windhorst, S. / Gabdulkhakov, A. / Weber, W. / Betzel, C.
History
DepositionSep 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,05411
Polymers36,0901
Non-polymers96510
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-44 kcal/mol
Surface area12920 Å2
Unit cell
Length a, b, c (Å)59.902, 85.747, 130.747
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21A-598-

HOH

31A-677-

HOH

41A-779-

HOH

51A-780-

HOH

61A-792-

HOH

71A-807-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkaline serine protease


Mass: 36089.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Gene: StmPr1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93IQ4

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Non-polymers , 5 types, 330 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.9 M Ammonium sulfate 0.4 M Lithium sulfate 0.1 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.89→49.154 Å / Num. obs: 54075 / % possible obs: 99.7 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.045 / Rrim(I) all: 0.121 / Net I/σ(I): 11.6
Reflection shellResolution: 1.89→2.03 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 5384 / CC1/2: 0.96 / Rpim(I) all: 0.169 / Rrim(I) all: 0.446 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→49.154 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.959 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.15 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1062 3.886 %RANDOM
Rwork0.1747 26268 --
all0.177 ---
obs-27330 99.843 %-
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: 28.394 Å2
Baniso -1Baniso -2Baniso -3
1--1.718 Å2-0 Å20 Å2
2--3.997 Å2-0 Å2
3----2.279 Å2
Refinement stepCycle: LAST / Resolution: 1.89→49.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 55 320 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122629
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.7613589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.045355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.69510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59110339
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.35710100
X-RAY DIFFRACTIONr_chiral_restr0.1110.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022063
X-RAY DIFFRACTIONr_nbd_refined0.2240.21433
X-RAY DIFFRACTIONr_nbtor_refined0.310.21818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2301
X-RAY DIFFRACTIONr_metal_ion_refined0.1550.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.224
X-RAY DIFFRACTIONr_mcbond_it2.4172.5771423
X-RAY DIFFRACTIONr_mcangle_it3.2314.6171777
X-RAY DIFFRACTIONr_scbond_it3.442.8261206
X-RAY DIFFRACTIONr_scangle_it4.6365.0431812
X-RAY DIFFRACTIONr_lrange_it5.9728.4134372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.9390.268780.2551925X-RAY DIFFRACTION99.4045
1.939-1.9920.273750.2461856X-RAY DIFFRACTION99.9482
1.992-2.050.376730.2231797X-RAY DIFFRACTION99.8932
2.05-2.1130.274720.2221775X-RAY DIFFRACTION99.6762
2.113-2.1820.199690.1871719X-RAY DIFFRACTION99.9441
2.182-2.2580.261670.1891653X-RAY DIFFRACTION99.8839
2.258-2.3430.23640.1791592X-RAY DIFFRACTION99.759
2.343-2.4390.232620.1781540X-RAY DIFFRACTION99.9376
2.439-2.5470.268600.1841485X-RAY DIFFRACTION99.8707
2.547-2.6710.266570.181413X-RAY DIFFRACTION99.661
2.671-2.8150.266550.1821364X-RAY DIFFRACTION100
2.815-2.9850.265520.1821288X-RAY DIFFRACTION100
2.985-3.190.266490.1771213X-RAY DIFFRACTION99.9208
3.19-3.4450.214460.161135X-RAY DIFFRACTION99.8309
3.445-3.7720.18430.1391053X-RAY DIFFRACTION100
3.772-4.2140.153380.129943X-RAY DIFFRACTION99.8982
4.214-4.860.165350.121854X-RAY DIFFRACTION100
4.86-5.9370.209290.162730X-RAY DIFFRACTION100
5.937-8.3360.229230.185575X-RAY DIFFRACTION99.8331
8.336-49.1540.311150.189354X-RAY DIFFRACTION99.7297

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