+Open data
-Basic information
Entry | Database: PDB / ID: 2w7u | ||||||
---|---|---|---|---|---|---|---|
Title | SplA serine protease of Staphylococcus aureus (2.4A) | ||||||
Components | SERINE PROTEASE SPLA | ||||||
Keywords | HYDROLASE / FAMILY S1 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Stec-Niemczyka, J. / Pustelny, K. / Kisielewska, M. / Bista, M. / Boulware, K.T. / Stennicke, H.R. / Thogersen, I.B. / Daugherty, P.S. / Enghild, J.J. / Popowicz, G.M. ...Stec-Niemczyka, J. / Pustelny, K. / Kisielewska, M. / Bista, M. / Boulware, K.T. / Stennicke, H.R. / Thogersen, I.B. / Daugherty, P.S. / Enghild, J.J. / Popowicz, G.M. / Dubin, A. / Potempa, J. / Dubin, G. | ||||||
Citation | Journal: Biochem.J. / Year: 2009 Title: Structural and Functional Characterization of Spla, an Exclusively Specific Protease of Staphylococcus Aureus. Authors: Stec-Niemczyk, J. / Pustelny, K. / Kisielewska, M. / Bista, M. / Boulware, K.T. / Stennicke, H.R. / Thogersen, I.B. / Daugherty, P.S. / Enghild, J.J. / Baczynski, K. / Popowicz, G.M. / ...Authors: Stec-Niemczyk, J. / Pustelny, K. / Kisielewska, M. / Bista, M. / Boulware, K.T. / Stennicke, H.R. / Thogersen, I.B. / Daugherty, P.S. / Enghild, J.J. / Baczynski, K. / Popowicz, G.M. / Dubin, A. / Potempa, J. / Dubin, G. #1: Journal: J.Mol.Biol. / Year: 2006 Title: Functional and Structural Characterization of Spl Proteases from Staphylococcus Aureus. Authors: Popowicz, G.M. / Dubin, G. / Stec-Niemczyk, J. / Czarny, A. / Dubin, A. / Potempa, J. / Holak, T.A. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -5-STRANDED BARREL THIS IS REPRESENTED BY A -4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2w7u.cif.gz | 156.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2w7u.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 2w7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/2w7u ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w7u | HTTPS FTP |
---|
-Related structure data
Related structure data | 2w7sC 2as9S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21885.482 Da / Num. of mol.: 4 / Fragment: RESIDUES 36-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 8325-4 / Tissue: EXTRACELLULARGlossary of biology / Plasmid: PWB980 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): WB800 / References: UniProt: Q2FXC2, glutamyl endopeptidase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.02 % / Description: NONE |
---|---|
Crystal grow | Details: 0.2M SODIUM FORMATE, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 294 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2007 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→20 Å / Num. obs: 30882 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.43→2.56 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.1 / % possible all: 97.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AS9 Resolution: 2.43→19.87 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.406 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES AND SIDE CHAINS NOT DEFINED BY ELECTRON DENISTY WERE OMITTED FORM MODEL.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.65 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→19.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|