[English] 日本語
Yorodumi- PDB-6p4r: Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p4r | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-2-6-Gal-beta-1-4-GlcNAc glycans | |||||||||||||||
Components | Putative pertussis-like toxin subunit | |||||||||||||||
Keywords | TOXIN / PltB | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | |||||||||||||||
Authors | Nguyen, T. / Milano, S.K. / Hillpot, E.C. / Yang, Y.A. / Song, J. | |||||||||||||||
Funding support | United States, 4items
| |||||||||||||||
Citation | Journal: Cell Host Microbe / Year: 2020 Title: Salmonella Typhoid Toxin PltB Subunit and Its Non-typhoidal Salmonella Ortholog Confer Differential Host Adaptation and Virulence. Authors: Lee, S. / Yang, Y.A. / Milano, S.K. / Nguyen, T. / Ahn, C. / Sim, J.H. / Thompson, A.J. / Hillpot, E.C. / Yoo, G. / Paulson, J.C. / Song, J. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6p4r.cif.gz | 135 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6p4r.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 6p4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p4r_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6p4r_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6p4r_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 6p4r_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/6p4r ftp://data.pdbj.org/pub/pdb/validation_reports/p4/6p4r | HTTPS FTP |
-Related structure data
Related structure data | 6p4mC 6p4nC 6p4pC 6p4qC 6p4sC 6p4tC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16320.479 Da / Num. of mol.: 5 / Mutation: N29K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) Gene: STY1891, t1107 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Z6A3 #2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.77 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG1500, Sodium actetate pH 4.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPic-6000HE / Detector: PIXEL / Date: Apr 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→27.3981 Å / Num. obs: 58793 / % possible obs: 99.7 % / Redundancy: 3.7 % / Net I/σ(I): 16.25 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 2.9 % / Num. unique obs: 5882 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→27.395 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→27.395 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|