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Yorodumi- PDB-5tj2: Gasdermin-B C-terminal domain containing the polymorphism residue... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tj2 | |||||||||
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Title | Gasdermin-B C-terminal domain containing the polymorphism residues Gly299:Ser306 fused to maltose binding protein | |||||||||
Components | Sugar ABC transporter substrate-binding protein,Gasdermin-B fusion protein | |||||||||
Keywords | LIPID BINDING PROTEIN / alpha helices / fusion protein / C-terminal domain / 1 SNP | |||||||||
Function / homology | Function and homology information cytotoxic T cell pyroptotic cell death / wide pore channel activity / killing by host of symbiont cells / programmed cell death / cardiolipin binding / phosphatidylinositol-4-phosphate binding / pyroptotic inflammatory response / phosphatidylserine binding / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding ...cytotoxic T cell pyroptotic cell death / wide pore channel activity / killing by host of symbiont cells / programmed cell death / cardiolipin binding / phosphatidylinositol-4-phosphate binding / pyroptotic inflammatory response / phosphatidylserine binding / phosphatidylinositol-4,5-bisphosphate binding / phospholipid binding / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to bacterium / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | |||||||||
Authors | Chao, L.K. / Herzberg, O. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2017 Title: Human Gasdermin-B and disease: Sulfatide Binding, Caspase cleavage, and Structural impact of Asthma- and IBS-Associated Polymorphism Authors: Chao, L.K. / Kulakova, L. / Herzberg, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tj2.cif.gz | 402.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tj2.ent.gz | 326.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tj2_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5tj2_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5tj2_validation.xml.gz | 67.7 KB | Display | |
Data in CIF | 5tj2_validation.cif.gz | 94.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/5tj2 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tj2 | HTTPS FTP |
-Related structure data
Related structure data | 5tibSC 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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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | Monomer as determined by size exclusion chromatography |
-Components
#1: Protein | Mass: 60461.555 Da / Num. of mol.: 4 / Mutation: P1306S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: malE, OO96_18925, GSDMB, GSDML, PP4052, PRO2521 / Plasmid: plasmid / Details (production host): pMALX(E) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178SBV6, UniProt: Q8TAX9 #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #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: 2.91 Å3/Da / Density % sol: 57.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6 / Details: 2.1 M sodium malonate, 10 mM EDTA / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42.5 Å / Num. obs: 65695 / % possible obs: 99.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 11.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TIB Resolution: 2.8→42.5 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.354 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 239.9 Å2 / Biso mean: 64.283 Å2 / Biso min: 18.08 Å2
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Refinement step | Cycle: final / Resolution: 2.8→42.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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