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Yorodumi- PDB-4k1s: Gly-Ser-SplB protease from Staphylococcus aureus at 1.96 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k1s | ||||||
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Title | Gly-Ser-SplB protease from Staphylococcus aureus at 1.96 A resolution | ||||||
Components | Serine protease SplB | ||||||
Keywords | HYDROLASE / chymotrypsin-like fold / serine protease / extracellular | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Zdzalik, M. / Pustelny, K. / Stec-Niemczyk, J. / Cichon, P. / Czarna, A. / Popowicz, G. / Drag, M. / Wladyka, B. / Potempa, J. / Dubin, A. / Dubin, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Staphylococcal SplB Serine Protease Utilizes a Novel Molecular Mechanism of Activation. Authors: Pustelny, K. / Zdzalik, M. / Stach, N. / Stec-Niemczyk, J. / Cichon, P. / Czarna, A. / Popowicz, G. / Mak, P. / Drag, M. / Salvesen, G.S. / Wladyka, B. / Potempa, J. / Dubin, A. / Dubin, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k1s.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k1s.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 4k1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/4k1s ftp://data.pdbj.org/pub/pdb/validation_reports/k1/4k1s | HTTPS FTP |
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-Related structure data
Related structure data | 4k1tC 2w7sS 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
#1: Protein | Mass: 22546.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: splB, SAOUHSC_01941 / Production host: Escherichia coli (E. coli) References: UniProt: Q2FXC3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→22.97 Å / Num. obs: 32322 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W7S Resolution: 1.96→22.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.611 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.384 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→22.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.011 Å / Total num. of bins used: 20
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