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- PDB-6sf7: Atomic resolution structure of SplF protease from Staphylococcus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sf7 | ||||||
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Title | Atomic resolution structure of SplF protease from Staphylococcus aureus | ||||||
![]() | Serine protease SplF | ||||||
![]() | HYDROLASE / Virulence factor / protease / bacterial | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Golik, P. / Stach, N. / Karim, A. / Dubin, G. | ||||||
![]() | ![]() Title: Structural Determinants of Substrate Specificity of SplF Protease from Staphylococcus aureus . Authors: Stach, N. / Karim, A. / Golik, P. / Kitel, R. / Pustelny, K. / Gruba, N. / Groborz, K. / Jankowska, U. / Kedracka-Krok, S. / Wladyka, B. / Drag, M. / Lesner, A. / Dubin, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 315.6 KB | Display | ![]() |
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PDB format | ![]() | 256.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.1 KB | Display | ![]() |
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Full document | ![]() | 504.2 KB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4vidS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 22045.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: splF, SAUSA300_1753 / Production host: ![]() ![]() References: UniProt: Q2FFT4, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Non-polymers , 5 types, 469 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32.5 % PEG 400, 0.3 M Ammonium Sulphate pH = 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 77687 / % possible obs: 92.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 13.9 / Num. unique obs: 10882 / % possible all: 88.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4VID Resolution: 1.7→29.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.79 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.7 Å2 / Biso mean: 27.698 Å2 / Biso min: 13.73 Å2
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Refinement step | Cycle: final / Resolution: 1.7→29.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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