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Yorodumi- PDB-2vid: Serine protease SplB from Staphylococcus aureus at 1.8A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vid | ||||||
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Title | Serine protease SplB from Staphylococcus aureus at 1.8A resolution | ||||||
Components | SERINE PROTEASE SPLB | ||||||
Keywords | HYDROLASE / PROTEASE / SERINE PROTEASE / STAPHYLOCOCCUS AUREUS | ||||||
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 | Dubin, G. / Stec-Niemczyk, J. / Kisielewska, M. / Pustelny, K. / Popowicz, G.M. / Bista, M. / Kantyka, T. / Boulware, K.T. / Stennicke, H.R. / Czarna, A. ...Dubin, G. / Stec-Niemczyk, J. / Kisielewska, M. / Pustelny, K. / Popowicz, G.M. / Bista, M. / Kantyka, T. / Boulware, K.T. / Stennicke, H.R. / Czarna, A. / Phopaisarn, M. / Daugherty, P.S. / Thogersen, I.B. / Enghild, J.J. / Thornberry, N. / Dubin, A. / Potempa, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Enzymatic Activity of the Staphylococcus Aureus Splb Serine Protease is Induced by Substrates Containing the Sequence Trp-Glu-Leu-Gln. Authors: Dubin, G. / Stec-Niemczyk, J. / Kisielewska, M. / Pustelny, K. / Popowicz, G.M. / Bista, M. / Kantyka, T. / Boulware, K.T. / Stennicke, H.R. / Czarna, A. / Phopaisarn, M. / Daugherty, P.S. / ...Authors: Dubin, G. / Stec-Niemczyk, J. / Kisielewska, M. / Pustelny, K. / Popowicz, G.M. / Bista, M. / Kantyka, T. / Boulware, K.T. / Stennicke, H.R. / Czarna, A. / Phopaisarn, M. / Daugherty, P.S. / Thogersen, I.B. / Enghild, J.J. / Thornberry, N. / Dubin, A. / Potempa, J. #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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" AND "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 "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-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 | 2vid.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vid.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/2vid ftp://data.pdbj.org/pub/pdb/validation_reports/vi/2vid | HTTPS FTP |
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-Related structure data
Related structure data | 2as9S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22402.086 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 8325-4 / Plasmid: PWB980 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): WB800 / References: UniProt: Q9KH50, UniProt: Q2FXC3*PLUS #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: 2.69 Å3/Da / Density % sol: 53.96 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: SITTING DROP VAPOR DIFFUSION; 20C; GROWN BY MIXING EQUAL VOLUMES OF SPLB (35 MG/ML IN 5MM TRIS-HCL, PH 8.0 CONTAINING 50MM NACL) AND 0.1M TRIS-HCL, PH 8.5-9.0 CONTAINING 30% PEG 3350 ...Details: SITTING DROP VAPOR DIFFUSION; 20C; GROWN BY MIXING EQUAL VOLUMES OF SPLB (35 MG/ML IN 5MM TRIS-HCL, PH 8.0 CONTAINING 50MM NACL) AND 0.1M TRIS-HCL, PH 8.5-9.0 CONTAINING 30% PEG 3350 (OPTIMIZED HAMPTON RESEARCH INDEX SOLUTION NUMBER 45) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 48001 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 14.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.2 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AS9 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.834 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE EXCLUDED FROM THE MODEL. AUTHOR SUGGESTS TO RETAIN THE ORIGINAL WATERS AND NOT TO MOVE THEM TO SYMMETRY RELATED 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: 26.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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