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- PDB-7skm: Complex between S. aureus aureolysin and wt IMPI. -

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Basic information

Entry
Database: PDB / ID: 7skm
TitleComplex between S. aureus aureolysin and wt IMPI.
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 ...: / 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
DI(HYDROXYETHYL)ETHER / Zinc metalloproteinase aureolysin / Inducible metalloproteinase inhibitor protein
Similarity search - Component
Biological speciesGalleria mellonella (greater wax moth)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)83,38519
Polymers82,6166
Non-polymers77013
Water12,773709
1
A: Zinc metalloproteinase aureolysin
B: IMPI alpha
E: IMPI alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6189
Polymers41,3083
Non-polymers3106
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)41,76810
Polymers41,3083
Non-polymers4607
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.140, 68.140, 166.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
32B
42D
53E
63F

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAGLYGLYAA209 - 5071 - 299
211ALAALAGLYGLYCD209 - 5071 - 299
322ILEILEASNASNBB20 - 564 - 40
422ILEILEASNASNDE20 - 564 - 40
533ILEILEPROPROEC57 - 841 - 28
633ILEILEPROPROFF57 - 841 - 28

NCS ensembles :
IDDetails
1Global NCS restraints between domains: 1 2
2Global NCS restraints between domains: 3 4
3Global NCS restraints between domains: 5 6

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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 natural source / Source: (natural) Staphylococcus aureus (bacteria) / 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: 3684.299 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

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Non-polymers , 5 types, 722 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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase: ...Details: Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees 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.

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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, L10.5099
pseudo-merohedral22-K, -H, -L20.4901
ReflectionResolution: 1.85→52.7 Å / Num. obs: 64323 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 42.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.042 / Net I/σ(I): 14.7
Reflection shellResolution: 1.85→1.96 Å / Rmerge(I) obs: 2.772 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 10209 / CC1/2: 0.63 / Rpim(I) all: 0.788

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Processing

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

1bqb

3ssb


Resolution: 1.85→52.689 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.634 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.027 / ESU R Free: 0.028 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2186 724 1.126 %
Rwork0.1644 63598 -
all0.165 --
obs-64322 99.966 %
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: 38.072 Å2
Baniso -1Baniso -2Baniso -3
1-11.211 Å20 Å20 Å2
2--11.211 Å20 Å2
3----22.422 Å2
Refinement stepCycle: LAST / Resolution: 1.85→52.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 34 709 6451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125898
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.647921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5825.28339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59815924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4651516
X-RAY DIFFRACTIONr_chiral_restr0.1430.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024638
X-RAY DIFFRACTIONr_nbd_refined0.1590.22688
X-RAY DIFFRACTIONr_nbtor_refined0.2760.23928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2433
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0940.234
X-RAY DIFFRACTIONr_mcbond_it1.7873.2382947
X-RAY DIFFRACTIONr_mcangle_it2.544.8483652
X-RAY DIFFRACTIONr_scbond_it1.9743.4482951
X-RAY DIFFRACTIONr_scangle_it2.8025.0944269
X-RAY DIFFRACTIONr_lrange_it5.05544.7788902
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Weight Biso : 0.5 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDRms dev Biso (Å2)Rms dev position (Å)
11A3.73140.07332
12C3.73140.07332
23B2.106730.06946
24D2.106730.06946
35E3.60680.06586
36F3.60680.06586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.24490.2084684X-RAY DIFFRACTION99.6211
1.898-1.950.287480.2274588X-RAY DIFFRACTION100
1.95-2.0060.278590.2134465X-RAY DIFFRACTION100
2.006-2.0680.216570.2114301X-RAY DIFFRACTION100
2.068-2.1360.301550.2034159X-RAY DIFFRACTION99.9763
2.136-2.2110.235460.1844071X-RAY DIFFRACTION100
2.211-2.2940.225510.173878X-RAY DIFFRACTION100
2.294-2.3880.217460.1573743X-RAY DIFFRACTION100
2.388-2.4940.233360.1723647X-RAY DIFFRACTION100
2.494-2.6150.234220.1793480X-RAY DIFFRACTION100
2.615-2.7570.217330.1683283X-RAY DIFFRACTION100
2.757-2.9240.203390.1813105X-RAY DIFFRACTION100
2.924-3.1250.22440.1832912X-RAY DIFFRACTION100
3.125-3.3750.3210.1662733X-RAY DIFFRACTION100
3.375-3.6960.224230.142509X-RAY DIFFRACTION100
3.696-4.1310.128360.1352257X-RAY DIFFRACTION100
4.131-4.7670.188320.1342002X-RAY DIFFRACTION100
4.767-5.8310.234100.1411710X-RAY DIFFRACTION100
5.831-8.2160.3940.1591330X-RAY DIFFRACTION100
8.216-52.6890.256130.173741X-RAY DIFFRACTION99.6037
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)
10.24360.0719-0.11690.03550.01910.3312-0.00210.0172-0.0220.00580.0035-0.00480.0010.009-0.00140.0142-0.00510.00690.009-0.01070.076730.7342-9.8104-16.3261
20.65790.40930.36470.25630.22620.2207-0.0054-0.0676-0.0047-0.005-0.0326-0.0053-0.0012-0.04510.0380.0025-0.00130.00620.0405-0.01920.080910.0072-16.0277-30.6866
30.1088-0.0452-0.07680.1032-0.15920.50070.0017-0.00480.0129-0.01030.0178-0.0010.0339-0.0393-0.01950.0202-0.00290.00320.01230.01010.07852.4289-42.9102-24.3399
40.6006-0.20710.47481.1797-0.63180.5738-0.03050.04430.0052-0.0904-0.0299-0.12150.02170.04180.06040.02630.00050.02560.00440.0090.0723.5059-50.4079-10.8911
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 - 508
5X-RAY DIFFRACTION4ALLD20 - 56
6X-RAY DIFFRACTION4ALLF57 - 85

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