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Yorodumi- PDB-4k1t: Gly-Ser-SplB protease from Staphylococcus aureus at 1.60 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k1t | ||||||
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Title | Gly-Ser-SplB protease from Staphylococcus aureus at 1.60 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: 1.6 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 | 4k1t.cif.gz | 150.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k1t.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k1t_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 4k1t_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 4k1t_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 4k1t_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/4k1t ftp://data.pdbj.org/pub/pdb/validation_reports/k1/4k1t | HTTPS FTP |
-Related structure data
Related structure data | 4k1sC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22546.217 Da / Num. of mol.: 3 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: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.76 Å3/Da / Density % sol: 55.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.01M Zinc sulfate heptahydrate, 0.1M MES monohydrate pH 6.5, 25% v/v Polyethylene glycol monomethyl ether 550, 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 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→18.91 Å / Num. obs: 81007 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W7S Resolution: 1.6→18.91 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 1.456 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / 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: 13.585 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→18.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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