+Open data
-Basic information
Entry | Database: PDB / ID: 7skm | ||||||
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Title | Complex between S. aureus aureolysin and wt IMPI. | ||||||
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 | Galleria mellonella (greater wax moth) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 7skm.cif.gz | 286.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7skm.ent.gz | 219.8 KB | Display | PDB format |
PDBx/mmJSON format | 7skm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7skm_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 7skm_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 7skm_validation.xml.gz | 35 KB | Display | |
Data in CIF | 7skm_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/7skm ftp://data.pdbj.org/pub/pdb/validation_reports/sk/7skm | HTTPS FTP |
-Related structure data
Related structure data | 7sklC 1bqbS 3ssbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1
NCS ensembles :
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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 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 | 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: 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 / #5: Chemical | #6: Chemical | #7: Chemical | #8: 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: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 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. |
-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: 1.85→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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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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: 38.072 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→52.689 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Weight Biso : 0.5 / Weight position: 0.05
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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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