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Yorodumi- PDB-3zhn: Crystal structure of the T6SS lipoprotein TssJ1 from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zhn | |||||||||
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Title | Crystal structure of the T6SS lipoprotein TssJ1 from Pseudomonas aeruginosa | |||||||||
Components | PA_0080 | |||||||||
Keywords | TOXIN / PATHOGEN / TYPE VI SECRETION SYSTEM | |||||||||
Function / homology | Type VI secretion system, lipoprotein SciN / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Immunoglobulin-like / Sandwich / Mainly Beta / IODIDE ION / Uncharacterized protein Function and homology information | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.4 Å | |||||||||
Authors | Robb, C.S. / Assmus, M. / Nano, F.E. / Boraston, A.B. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of the T6Ss Lipoprotein Tssj1 from Pseudomonas Aeruginosa. Authors: Robb, C.S. / Assmus, M. / Nano, F.E. / Boraston, A.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zhn.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zhn.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 3zhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zhn ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zhn | 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: 17564.656 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I752 | ||
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#2: Chemical | ChemComp-IOD / #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 Å3/Da / Density % sol: 38 % / Description: NONE |
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Crystal grow | Details: 0.2M FORMATE, 15% PEG 5K MME |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 1, 2011 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→19.24 Å / Num. obs: 24682 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 9.27 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.61 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.4→22.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.302 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
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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: 16.635 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→22.75 Å
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