+Open data
-Basic information
Entry | Database: PDB / ID: 5y0e | |||||||||
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Title | Crystal structure of TssK | |||||||||
Components | TssK | |||||||||
Keywords | STRUCTURAL PROTEIN / baseplate | |||||||||
Function / homology | Type VI secretion system TssK / Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE / TssK Function and homology information | |||||||||
Biological species | Serratia sp. FS14 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | |||||||||
Authors | Tong, H. / Xu, D. / Ran, T. / Wang, W.W. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Structure of TssK at 2.5 Angstroms resolution. Authors: Xu, D. / Tong, H. / Ran, T. / Wang, W.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y0e.cif.gz | 262.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y0e.ent.gz | 212.5 KB | Display | PDB format |
PDBx/mmJSON format | 5y0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y0e_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 5y0e_full_validation.pdf.gz | 490 KB | Display | |
Data in XML | 5y0e_validation.xml.gz | 48.3 KB | Display | |
Data in CIF | 5y0e_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/5y0e ftp://data.pdbj.org/pub/pdb/validation_reports/y0/5y0e | HTTPS FTP |
-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: 51482.719 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia sp. FS14 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3F2YLT8*PLUS #2: Chemical | ChemComp-SO4 / #3: 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: 3.37 Å3/Da / Density % sol: 63.54 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.75 / Details: PEG4000, Li2SO4, 2-Proponal |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 74200 / % possible obs: 99.8 % / Redundancy: 40 % / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 41 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→19.97 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.97 Å
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Refine LS restraints |
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LS refinement shell |
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