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Yorodumi- PDB-6tyn: Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-3-G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tyn | |||||||||||||||
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Title | Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans | |||||||||||||||
Components | Pertussis like toxin subunit B | |||||||||||||||
Keywords | TOXIN / PltB | |||||||||||||||
Function / homology | Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / extracellular region / Mainly Beta / Pertussis-like toxin subunit Function and homology information | |||||||||||||||
Biological species | Salmonella typhi (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | |||||||||||||||
Authors | Nguyen, T. / Milano, S.K. / Yang, Y.A. / Song, J. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Plos Pathog. / Year: 2020 Title: The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication. Authors: Nguyen, T. / Lee, S. / Yang, Y.A. / Ahn, C. / Sim, J.H. / Kei, T.G. / Barnard, K.N. / Yu, H. / Millano, S.K. / Chen, X. / Parrish, C.R. / Song, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tyn.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tyn.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 6tyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tyn_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6tyn_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6tyn_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 6tyn_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/6tyn ftp://data.pdbj.org/pub/pdb/validation_reports/ty/6tyn | HTTPS FTP |
-Related structure data
Related structure data | 6tyoC 6tyqC 4rhrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12563.042 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhi (bacteria) Gene: STY1891, t1107, ABP05_22510, AXU46_23480, E2E79_23180, E2E83_22990, E2F00_23020, E2F08_23180, E2F09_23155, E2F13_22745, PltB Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Z6A3 #2: Polysaccharide | 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D- ...9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.71 Å3/Da / Density % sol: 54.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 26% PEG-1500, 0.1M Sodium Acetate pH 4.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.87 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→40 Å / Num. obs: 27512 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 37.4 |
Reflection shell | Resolution: 2.33→2.39 Å / Rmerge(I) obs: 0.526 / Num. unique obs: 2036 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RHR Resolution: 2.33→40 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 2.33→40 Å
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