[English] 日本語
Yorodumi- PDB-4ink: Crystal structure of SplD protease from Staphylococcus aureus at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ink | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SplD protease from Staphylococcus aureus at 1.56 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: 1.56 Å | ||||||
Authors | Zdzalik, M. / Kalinska, M. / Cichon, P. / Wysocka, M. / Stec-Niemczyk, J. / Stennicke, H.R. / Jabaiah, A. / Markiewicz, M. / Wladyka, B. / Daugherty, P.S. ...Zdzalik, M. / Kalinska, M. / Cichon, P. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ink.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ink.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ink.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4ink ftp://data.pdbj.org/pub/pdb/validation_reports/in/4ink | HTTPS FTP |
---|
-Related structure data
Related structure data | 4inlC 2w7sS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-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 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30-33% PEG2000 MME, 0.1-0.5 M potassium thiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→27.76 Å / Num. obs: 32697 / % possible obs: 98.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.56→1.65 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.1 / % possible all: 94.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W7S Resolution: 1.56→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.217 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.287 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|