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Yorodumi- PDB-6yv6: Crystal Structure of Serine protease SplB N2K/N3Q/S154R from Stap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yv6 | ||||||
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Title | Crystal Structure of Serine protease SplB N2K/N3Q/S154R from Staphylococcus aureus | ||||||
Components | Serine protease | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Spl / serine protease-like | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å | ||||||
Authors | Rangel Pereira, M.R. / Brear, P. / Knyphausen, P. / Jermutus, L. / Hollfelder, F. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: to be published Title: Crystal Structure of Serine protease SplB N2K/N3Q/S154R from Staphylococcus aureus Authors: Knyphausen, P. / Rangel Pereira, M.R. / Brear, P. / Jermutus, L. / Hollfelder, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yv6.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yv6.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 6yv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yv6_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 6yv6_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 6yv6_validation.xml.gz | 11 KB | Display | |
Data in CIF | 6yv6_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/6yv6 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/6yv6 | HTTPS FTP |
-Related structure data
Related structure data | 2vidS 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
#1: Protein | Mass: 22645.434 Da / Num. of mol.: 1 / Fragment: SPLB PROTEASE / Mutation: N2K/N3Q/S154R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: splB / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A2D1PJH6, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.37 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350 30%, TRIS-Cl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.36→32.63 Å / Num. obs: 37738 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Net I/σ(I): 15.2 / Num. measured all: 271636 / Scaling rejects: 18 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.6 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VID Resolution: 1.36→19.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.059 / SU Rfree Cruickshank DPI: 0.06
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Displacement parameters | Biso max: 110.34 Å2 / Biso mean: 28.11 Å2 / Biso min: 13.03 Å2
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Refinement step | Cycle: final / Resolution: 1.36→19.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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