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Yorodumi- PDB-7edd: Crystal structure of a serine protease from Streptococcus pyogenes -
+Open data
-Basic information
Entry | Database: PDB / ID: 7edd | ||||||
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Title | Crystal structure of a serine protease from Streptococcus pyogenes | ||||||
Components | C5a peptidase | ||||||
Keywords | LYASE / Subtilisin like / Cell adhesion / Protease | ||||||
Function / homology | Function and homology information C5a peptidase / serine-type endopeptidase activity / proteolysis / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.897 Å | ||||||
Authors | Jobichen, C. / Sivaraman, J. | ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: The Autocatalytic Cleavage Domain Is Not Required for the Activity of ScpC, a Virulence Protease from Streptococcus pyogenes : A Structural Insight. Authors: Jobichen, C. / Ying Chong, T. / Hui Ling, T. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7edd.cif.gz | 293.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7edd.ent.gz | 226.8 KB | Display | PDB format |
PDBx/mmJSON format | 7edd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7edd_validation.pdf.gz | 477.7 KB | Display | wwPDB validaton report |
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Full document | 7edd_full_validation.pdf.gz | 503.6 KB | Display | |
Data in XML | 7edd_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 7edd_validation.cif.gz | 70.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/7edd ftp://data.pdbj.org/pub/pdb/validation_reports/ed/7edd | HTTPS FTP |
-Related structure data
Related structure data | 5xyrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 168207.438 Da / Num. of mol.: 1 / Mutation: deletions 214-274,527-532 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: scpC Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q3HV58, C5a peptidase |
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-Non-polymers , 7 types, 94 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-PEG / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.84 Å3/Da / Density % sol: 71.97 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.65 Details: 0.2 M MgCl Hexahydrate, 0.1 M Tris pH 8.65, 28% PEG 3500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.897→50 Å / Num. obs: 60944 / % possible obs: 100 % / Redundancy: 19 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.9→2.95 Å / Rmerge(I) obs: 0.96 / Num. unique obs: 2973 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XYR Resolution: 2.897→48.37 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.897→48.37 Å
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Refine LS restraints |
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LS refinement shell |
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