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

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Basic information

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


serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
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
Chem-BO2 / 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 5, 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)37,22910
Polymers36,1491
Non-polymers1,0819
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-44 kcal/mol
Surface area12820 Å2
Unit cell
Length a, b, c (Å)60.455, 86.776, 131.327
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-599-

HOH

21A-617-

HOH

31A-729-

HOH

41A-800-

HOH

51A-802-

HOH

61A-803-

HOH

71A-814-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkaline serine protease


Mass: 36148.566 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, 338 molecules

#2: Chemical ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB


Mass: 384.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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.: 329 / 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: 48.58 %
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 citrate

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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→46.45 Å / Num. obs: 105855 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.077 / Rrim(I) all: 0.15 / Net I/σ(I): 7.7
Reflection shellResolution: 1.89→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 10635 / CC1/2: 0.825 / Rpim(I) all: 0.331 / Rrim(I) all: 0.637 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→46.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25134 1094 -RANDOM
Rwork0.20756 ---
obs0.20847 54050 98.9 %-
Displacement parametersBiso mean: 29.125 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0 Å20 Å2
2--2.4 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.89→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 68 329 2932
LS refinement shellResolution: 1.89→2.03 Å /
Rfactor% reflection
Rfree0.562 -
Rwork0.539 -
obs-89.37 %

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