+Open data
-Basic information
Entry | Database: PDB / ID: 2w7s | ||||||
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Title | SplA serine protease of Staphylococcus aureus (1.8A) | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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-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. #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 |
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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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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 7-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w7s.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w7s.ent.gz | 125.6 KB | Display | PDB format |
PDBx/mmJSON format | 2w7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/2w7s ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w7s | HTTPS FTP |
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-Related structure data
Related structure data | 2w7uC 2as9S 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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2 |
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3 |
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4 |
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Unit cell |
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-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 / | |
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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: 2.28 Å3/Da / Density % sol: 45.69 % / Description: NONE |
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Crystal grow | Details: 0.1M HEPES PH 7.5, 0.2M (NH4)2SO4, 30% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 72964 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AS9 Resolution: 1.8→19.85 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.823 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.133 / 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.
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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: 24.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.85 Å
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Refine LS restraints |
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