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- PDB-9i67: StmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine se... -

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Basic information

Entry
Database: PDB / ID: 9i67
TitleStmPr1, Stenotrophomonas maltophilia Protease 1, 36 kDa alkine serine protease in complex with Chymostatin
ComponentsAlkaline serine protease
KeywordsHYDROLASE / alkaline serine protease / Chymostatin / 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 / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
: / Alkaline serine protease
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,73212
Polymers36,2321
Non-polymers1,50011
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-75 kcal/mol
Surface area13060 Å2
Unit cell
Length a, b, c (Å)60.459, 86.514, 132.329
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-741-

HOH

21A-777-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 304 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-A1I1B / (2~{S})-2-[[(1~{S})-1-[(6~{S})-2-azanyl-1,4,5,6-tetrahydropyrimidin-6-yl]-2-[[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-phenyl-propan-2-yl]amino]pentan-2-yl]amino]-2-oxidanylidene-ethyl]carbamoylamino]-3-phenyl-propanoic acid


Mass: 607.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H41N7O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293.15 K / Method: batch mode / 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: Jul 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 24332 / % possible obs: 98.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 11.3
Reflection shellResolution: 1.99→2.09 Å / Rmerge(I) obs: 0.457 / Num. unique obs: 3272

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLMdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→29.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21261 1171 -RANDOM
Rwork0.15137 ---
obs0.15427 22689 98.97 %-
Displacement parametersBiso mean: 19.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.99→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 93 293 2932
LS refinement shellResolution: 1.99→2.09 Å /
Rfactor% reflection
Rfree0.335 -
Rwork0.24 -
obs-93.89 %

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