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- PDB-9g8v: StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine se... -

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Basic information

Entry
Database: PDB / ID: 9g8v
TitleStmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease
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
Alkaline serine protease
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.637 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
DepositionJul 24, 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)36,6098
Polymers36,0001
Non-polymers6097
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-47 kcal/mol
Surface area12990 Å2
Unit cell
Length a, b, c (Å)60.385, 86.382, 131.573
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

21A-626-

HOH

31A-770-

HOH

41A-821-

HOH

51A-826-

HOH

61A-836-

HOH

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Components

#1: Protein Alkaline serine protease


Mass: 36000.496 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.8 M ammonium sulfate 0.1 M Tris

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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: 0.968 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.637→49.541 Å / Num. obs: 42779 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 17.53 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.05 / Rrim(I) all: 0.185 / Χ2: 0.96 / Net I/σ(I): 1.38
Reflection shellResolution: 1.637→1.665 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.322 / Num. unique obs: 2107 / CC1/2: 0.869 / Rpim(I) all: 0.377 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.637→49.541 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.002 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 2140 5.002 %RANDOM
Rwork0.1728 40639 --
all0.175 ---
obs-42779 99.993 %-
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: 20.041 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.637→49.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 33 360 2923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122652
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.7653636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6215362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.744511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12310351
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.66610103
X-RAY DIFFRACTIONr_chiral_restr0.1190.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022096
X-RAY DIFFRACTIONr_nbd_refined0.2090.21326
X-RAY DIFFRACTIONr_nbtor_refined0.310.21828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2269
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.234
X-RAY DIFFRACTIONr_mcbond_it1.6291.7251439
X-RAY DIFFRACTIONr_mcangle_it2.2743.0941801
X-RAY DIFFRACTIONr_scbond_it2.7391.9441213
X-RAY DIFFRACTIONr_scangle_it3.8343.4751834
X-RAY DIFFRACTIONr_lrange_it4.6519.7564271
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.637-1.6790.2951500.26129610.26331110.9410.9521000.233
1.679-1.7250.2391570.23629060.23630630.9610.9621000.204
1.725-1.7750.2991400.2328180.23329580.9410.9641000.2
1.775-1.8290.2381580.20327290.20528880.9620.97299.96540.177
1.829-1.8890.2161400.18126600.18328000.9670.9781000.16
1.889-1.9560.2341390.18125620.18427010.9630.9791000.16
1.956-2.0290.2071370.16924600.17125970.9770.9821000.155
2.029-2.1120.2231310.17724000.1825310.9680.9821000.167
2.112-2.2060.2181270.16222790.16524060.9740.9851000.155
2.206-2.3130.1841040.15422120.15523160.980.9861000.144
2.313-2.4380.208920.15221110.15422030.9740.9861000.148
2.438-2.5850.211030.18219910.18320940.970.981000.176
2.585-2.7630.193940.17118960.17219900.9790.9831000.17
2.763-2.9840.2121000.17217150.17418150.9740.9821000.176
2.984-3.2680.205840.17516290.17717130.9730.9811000.185
3.268-3.6510.187750.1614640.16115390.980.9851000.169
3.651-4.2120.173670.13913150.1413820.9830.9891000.159
4.212-5.150.17600.1311190.13211790.9830.9911000.154
5.15-7.2440.191520.1938820.1939340.9790.9831000.226
7.244-49.5410.268300.2235300.2255610.9450.96999.82170.285

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