+Open data
-Basic information
Entry | Database: PDB / ID: 7skl | ||||||
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Title | Complex between S. aureus aureolysin and IMPI mutant I57I | ||||||
Components |
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Keywords | HYDROLASE / 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 | ||||||
Biological species | Staphylococcus aureus (bacteria) Galleria mellonella (greater wax moth) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mendes, S.R. / Eckhard, U. / Rodriguez-Banqueri, A. / Guevara, T. / Gomis-Ruth, F.X. | ||||||
Funding support | 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7skl.cif.gz | 269.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7skl.ent.gz | 206.3 KB | Display | PDB format |
PDBx/mmJSON format | 7skl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7skl_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
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Full document | 7skl_full_validation.pdf.gz | 4.8 MB | Display | |
Data in XML | 7skl_validation.xml.gz | 33.5 KB | Display | |
Data in CIF | 7skl_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/7skl ftp://data.pdbj.org/pub/pdb/validation_reports/sk/7skl | HTTPS FTP |
-Related structure data
Related structure data | 7skmC 1bqbS 3ssbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | 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 | 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 | 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 / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.35 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2020 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.642 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→68.08 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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