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- PDB-9i6c: StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine se... -

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Basic information

Entry
Database: PDB / ID: 9i6c
TitleStmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with Leupeptin
Components
  • Alkaline serine protease
  • Leupeptin
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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
DepositionJan 29, 2025Deposition 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
B: Leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2579
Polymers36,6442
Non-polymers6127
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-73 kcal/mol
Surface area12800 Å2
Unit cell
Length a, b, c (Å)60.78, 86.41, 132.35
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

21A-617-

HOH

31A-658-

HOH

41A-663-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Alkaline serine protease


Mass: 36231.785 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: Protein/peptide Leupeptin


Mass: 412.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 172 molecules

#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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.8 M Ammonium sulfate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.08→30 Å / Num. obs: 21042 / % possible obs: 98.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 8.9
Reflection shellResolution: 2.08→2.19 Å / Rmerge(I) obs: 0.569 / Num. unique obs: 2742

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
pointlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→29.64 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21772 1028 -RANDOM
Rwork0.16835 ---
obs0.17079 19969 98.58 %-
Displacement parametersBiso mean: 17.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2--0.16 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.08→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 32 165 2773
LS refinement shellResolution: 2.08→2.19 Å /
Rfactor% reflection
Rfree0.284 -
Rwork0.259 -
obs-85.56 %

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