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Yorodumi- PDB-4inl: Crystal structure of SplD protease from Staphylococcus aureus at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4inl | ||||||
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Title | Crystal structure of SplD protease from Staphylococcus aureus at 2.1 A resolution | ||||||
Components | Serine protease SplD | ||||||
Keywords | HYDROLASE / chymotrypsin-like protease / serine endopeptidase / extracellular staphylococcal proteases | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cichon, P. / Zdzalik, M. / Kalinska, M. / Wysocka, M. / Stec-Niemczyk, J. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Wladyka, B. / Daugherty, P.S. ...Cichon, P. / Zdzalik, M. / Kalinska, M. / Wysocka, M. / Stec-Niemczyk, J. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Wladyka, B. / Daugherty, P.S. / Lesner, A. / Rolka, K. / Dubin, A. / Potempa, J. / Dubin, G. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Biochemical and Structural Characterization of SplD Protease from Staphylococcus aureus. Authors: Zdzalik, M. / Kalinska, M. / Wysocka, M. / Stec-Niemczyk, J. / Cichon, P. / Stach, N. / Gruba, N. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Kedracka-Krok, S. / Wladyka, B. / ...Authors: Zdzalik, M. / Kalinska, M. / Wysocka, M. / Stec-Niemczyk, J. / Cichon, P. / Stach, N. / Gruba, N. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Kedracka-Krok, S. / Wladyka, B. / Daugherty, P.S. / Lesner, A. / Rolka, K. / Dubin, A. / Potempa, J. / Dubin, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4inl.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4inl.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 4inl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4inl ftp://data.pdbj.org/pub/pdb/validation_reports/in/4inl | HTTPS FTP |
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-Related structure data
Related structure data | 4inkC 2w7sS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22181.920 Da / Num. of mol.: 1 / Fragment: UNP residues 37-239 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: NCTC 8325 / Gene: SAOUHSC_01938, splD / Production host: Escherichia coli (E. coli) References: UniProt: Q2FXC5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine ED-2001, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→26.27 Å / Num. obs: 11885 / % possible obs: 86.7 % / Redundancy: 3 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 3.1 / % possible all: 72.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W7S Resolution: 2.1→24.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.831 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 30.587 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.41 Å
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