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- PDB-7skl: Complex between S. aureus aureolysin and IMPI mutant I57I -

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Basic information

Entry
Database: PDB / ID: 7skl
TitleComplex between S. aureus aureolysin and IMPI mutant I57I
Components
  • (IMPI alpha) x 2
  • Zinc metalloproteinase aureolysin
KeywordsHYDROLASE / Metallopeptidase / inhibitor complex / point mutant
Function / homology
Function and homology information


aureolysin / metalloendopeptidase inhibitor activity / anatomical structure morphogenesis / extracellular matrix organization / wound healing / metalloendopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / PepSY domain / Peptidase propeptide and YPEB domain / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Zinc metalloproteinase aureolysin / Inducible metalloproteinase inhibitor protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Galleria mellonella (greater wax moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMendes, S.R. / Eckhard, U. / Rodriguez-Banqueri, A. / Guevara, T. / Gomis-Ruth, F.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Comput Struct Biotechnol J / Year: 2022
Title: An engineered protein-based submicromolar competitive inhibitor of the Staphylococcus aureus virulence factor aureolysin
Authors: Mendes, S.R. / Eckhard, U. / Rodriguez-Banqueri, A. / Guevara, T. / Czermak, P. / Marcos, E. / Vilcinskas, A.
#1: Journal: Angew Chem Int Ed Engl / Year: 2011
Title: Structural evidence for standard-mechanism inhibition in metallopeptidases from a complex poised to resynthesize a peptide bond.
Authors: Arolas, J.L. / Botelho, T.O. / Vilcinskas, A. / Gomis-Ruth, F.X.
History
DepositionOct 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc metalloproteinase aureolysin
B: IMPI alpha
E: IMPI alpha
C: Zinc metalloproteinase aureolysin
D: IMPI alpha
F: IMPI alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,36519
Polymers82,6846
Non-polymers68213
Water10,070559
1
A: Zinc metalloproteinase aureolysin
B: IMPI alpha
E: IMPI alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,83812
Polymers41,3423
Non-polymers4969
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Zinc metalloproteinase aureolysin
D: IMPI alpha
F: IMPI alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5287
Polymers41,3423
Non-polymers1864
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.080, 68.080, 166.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Zinc metalloproteinase aureolysin / Staphylococcus aureus neutral proteinase


Mass: 33336.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: aur / Production host: unidentified (others) / References: UniProt: P81177, aureolysin

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Protein/peptide , 2 types, 4 molecules BDEF

#2: Protein/peptide IMPI alpha


Mass: 4286.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galleria mellonella (greater wax moth) / Gene: IMPI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P82176
#3: Protein/peptide IMPI alpha


Mass: 3718.315 Da / Num. of mol.: 2 / Mutation: I57F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galleria mellonella (greater wax moth) / Gene: IMPI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P82176

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Non-polymers , 4 types, 572 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor ...Details: Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.464
pseudo-merohedral22-K, -H, -L20.536
ReflectionResolution: 1.6→68.1 Å / Num. obs: 99152 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.029 / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 1.069 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 16384 / CC1/2: 0.999 / Rpim(I) all: 0.618 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SSB, 1BQB

3ssb

1bqb


Resolution: 1.6→68.08 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.656 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.016 / ESU R Free: 0.016 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1878 681 0.687 %
Rwork0.1579 98470 -
all0.158 --
obs-99151 99.706 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 32.642 Å2
Baniso -1Baniso -2Baniso -3
1-10.816 Å20 Å20 Å2
2--10.816 Å20 Å2
3----21.633 Å2
Refinement stepCycle: LAST / Resolution: 1.6→68.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5715 0 28 559 6302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125907
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.6427939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.565730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05825.277343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78715922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0141516
X-RAY DIFFRACTIONr_chiral_restr0.150.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024672
X-RAY DIFFRACTIONr_nbd_refined0.1750.22744
X-RAY DIFFRACTIONr_nbtor_refined0.2840.23943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2368
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0710.221
X-RAY DIFFRACTIONr_mcbond_it1.7812.8832947
X-RAY DIFFRACTIONr_mcangle_it2.4864.3213655
X-RAY DIFFRACTIONr_scbond_it2.0523.0712960
X-RAY DIFFRACTIONr_scangle_it2.8454.5354283
X-RAY DIFFRACTIONr_lrange_it4.48140.2038950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.255470.2537160X-RAY DIFFRACTION98.7801
1.642-1.6870.351470.227125X-RAY DIFFRACTION99.9164
1.687-1.7350.287470.2096925X-RAY DIFFRACTION99.9283
1.735-1.7890.264490.216714X-RAY DIFFRACTION99.9261
1.789-1.8470.226620.2076488X-RAY DIFFRACTION100
1.847-1.9120.24600.1886229X-RAY DIFFRACTION99.9682
1.912-1.9840.226340.1726127X-RAY DIFFRACTION99.9838
1.984-2.0650.192350.1715845X-RAY DIFFRACTION99.966
2.065-2.1570.204470.1695580X-RAY DIFFRACTION99.8935
2.157-2.2620.189320.1775355X-RAY DIFFRACTION99.6301
2.262-2.3840.337280.1785079X-RAY DIFFRACTION99.7851
2.384-2.5290.196260.1824891X-RAY DIFFRACTION99.8984
2.529-2.7030.15360.1714450X-RAY DIFFRACTION99.6003
2.703-2.9190.162340.1654242X-RAY DIFFRACTION99.5113
2.919-3.1980.226250.1513844X-RAY DIFFRACTION99.4857
3.198-3.5740.139130.1333533X-RAY DIFFRACTION99.6347
3.574-4.1250.121240.1153087X-RAY DIFFRACTION99.2345
4.125-5.0470.157150.1232616X-RAY DIFFRACTION99.1708
5.047-7.1190.12290.1582038X-RAY DIFFRACTION99.3207
7.119-68.080.218110.1411142X-RAY DIFFRACTION99.3109
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07640.0334-0.05110.025600.12150.00320.0014-0.00820.0032-0.00210.0036-0.0010.011-0.00120.001-0.00010.00380.009-0.00350.039830.5824-9.7607-16.3589
20.17550.09850.07730.08690.00940.07090.0045-0.01860.016-0.0042-0.00790.00890.0103-0.01080.00340.00210.0002-0.00240.0186-0.01190.036410.1165-15.9508-30.7375
30.045-0.042-0.0210.0513-0.02940.22460.00090.0017-0.0037-0.00330.00020.00840.0206-0.0077-0.00120.0072-0.00340.00150.0093-0.00350.0322.431-42.793-24.3753
40.3958-0.1840.09710.0949-0.06490.0816-0.01140.0210.0219-0.0017-0.0052-0.02040.002-0.00610.01660.0189-0.00490.00350.00440.00250.037122.9952-50.4506-10.9684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA209 - 509
2X-RAY DIFFRACTION2ALLB20 - 56
3X-RAY DIFFRACTION2ALLE57 - 86
4X-RAY DIFFRACTION3ALLC209 - 509
5X-RAY DIFFRACTION4ALLD20 - 56
6X-RAY DIFFRACTION4ALLF57 - 84

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