+Open data
-Basic information
Entry | Database: PDB / ID: 3sol | ||||||
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Title | Crystal structure of the type 2 secretion system pilotin GspS | ||||||
Components | Type II secretion pathway related proteinType II secretion system | ||||||
Keywords | PROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY / PILOTIN / SECRETIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Korotkov, K.V. / Hol, W.G.J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2013 Title: Crystal structure of the pilotin from the enterohemorrhagic Escherichia coli type II secretion system. Authors: Korotkov, K.V. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sol.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sol.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 3sol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/3sol ftp://data.pdbj.org/pub/pdb/validation_reports/so/3sol | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10873.412 Da / Num. of mol.: 1 / Fragment: unp residues 39-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECO57PM13, etpO, GSPS, L7044 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BSV3 | ||
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#2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M MG CHLORIDE, 0.1M TRIS-HCL, 30% PEG3350, pH 8.5, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 3, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→47.261 Å / Num. obs: 16858 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.384 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 24.39 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.01 / Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→47.26 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2004 / WRfactor Rwork: 0.1758 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8784 / SU B: 5.137 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1386 / SU Rfree: 0.1289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.44 Å2 / Biso mean: 38.1188 Å2 / Biso min: 10.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 35.825 Å / Origin y: 39.565 Å / Origin z: 4.402 Å
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