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Yorodumi- PDB-4ps2: Structure of the C-terminal fragment (87-165) of E.coli EAEC TssB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ps2 | ||||||
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Title | Structure of the C-terminal fragment (87-165) of E.coli EAEC TssB molecule | ||||||
Components | Putative type VI secretion proteinType VI secretion system | ||||||
Keywords | CONTRACTILE PROTEIN / helices bundle / T6SS contractile sheath / TssC | ||||||
Function / homology | Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / metal ion binding / Putative type VI secretion protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Douzi, B. / Logger, L. / Spinelli, S. / Blangy, S. / Cambillau, C. / Cascales, E. | ||||||
Citation | Journal: To be Published Title: Mapping the tube-sheath interface within the Type VI secretion system tail Authors: Douzi, B. / Logger, L. / Spinelli, S. / Blangy, S. / Cambillau, C. / Cascales, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ps2.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ps2.ent.gz | 31.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ps2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4ps2 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4ps2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 9279.812 Da / Num. of mol.: 1 / Fragment: UNP residues 88-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 042 / EAEC / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3GU37 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CL / |
#4: 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: 2.25 Å3/Da / Density % sol: 45.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Zinc acetate 0.2 M, PEG3350 20%, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2013 |
Radiation | Monochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 2→42 Å / Num. obs: 5921 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 28.11 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 5 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2 / Num. unique all: 1730 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→41.88 Å / Cor.coef. Fo:Fc: 0.9277 / Cor.coef. Fo:Fc free: 0.9224 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.206 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.24 Å / Total num. of bins used: 5
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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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