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Yorodumi- PDB-6iai: StoD is a novel Salmonella Typhi type III secretion system E3 ubi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iai | ||||||||||||
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Title | StoD is a novel Salmonella Typhi type III secretion system E3 ubiquitin ligase effector | ||||||||||||
Components | Protein of uncharacterized function (DUF1076) | ||||||||||||
Keywords | PROTEIN BINDING / salmonella T3SS effector ubiquitin ligase | ||||||||||||
Function / homology | Effector protein NleG / Effector protein NleG superfamily / Effector protein NleG / biological process involved in symbiotic interaction / ubiquitin-protein transferase activity / DUF1076 domain-containing protein Function and homology information | ||||||||||||
Biological species | Salmonella typhi (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.54 Å | ||||||||||||
Authors | McDowell, M.A. / Lea, S.M. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Life Sci Alliance / Year: 2019 Title: The S . Typhi effector StoD is an E3/E4 ubiquitin ligase which binds K48- and K63-linked diubiquitin. Authors: McDowell, M.A. / Byrne, A.M. / Mylona, E. / Johnson, R. / Sagfors, A. / Crepin, V.F. / Lea, S. / Frankel, G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iai.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iai.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 6iai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iai_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 6iai_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 6iai_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6iai_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/6iai ftp://data.pdbj.org/pub/pdb/validation_reports/ia/6iai | HTTPS FTP |
-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: 13896.517 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: STY1076, STY1076, t1865, NCTC8385_01041 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Z7T2 #2: 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: 3.03 Å3/Da / Density % sol: 59.43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 60% 0.9 M Na malonate, 0.5% Jeffamine, 0.1M HEPES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 23, 2013 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→34.65 Å / Num. obs: 23299 / % possible obs: 99.8 % / Redundancy: 26.1 % / Biso Wilson estimate: 61.89 Å2 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 2.54→2.61 Å |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.54→34.65 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.9114 / SU R Cruickshank DPI: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.343 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.242
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Displacement parameters | Biso mean: 54.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.365 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.54→34.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.65 Å / Total num. of bins used: 12
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