+Open data
-Basic information
Entry | Database: PDB / ID: 5kaz | ||||||
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Title | Human SH2D1B structure | ||||||
Components | SH2 domain-containing protein 1B | ||||||
Keywords | SIGNALING PROTEIN / SH2D1B / EAT2 / SLAM / SAP | ||||||
Function / homology | Function and homology information positive regulation of natural killer cell mediated immunity / leukocyte activation involved in immune response / positive regulation of innate immune response / regulation of immune response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein-macromolecule adaptor activity / adaptive immune response / innate immune response / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Taha, M. / Nezerwa, E. / Nam, H.-J. | ||||||
Citation | Journal: Protein Pept. Lett. / Year: 2016 Title: The X-ray Crystallographic Structure of Human EAT2 (SH2D1B). Authors: Taha, M. / Nezerwa, E. / Nam, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kaz.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kaz.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 5kaz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/5kaz ftp://data.pdbj.org/pub/pdb/validation_reports/ka/5kaz | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12098.149 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SH2D1B, EAT2 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O14796 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Na-Citrate pH 5.5, 24% PEG 4000, 50 mM (NH)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31.054 Å / Num. obs: 13571 / % possible obs: 98.8 % / Redundancy: 4.1 % / Net I/σ(I): 33.9 |
-Processing
Software |
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Refinement | Resolution: 1.7→35.191 Å / SU ML: 0.14 / σ(F): 1.5 / Phase error: 22.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.191 Å
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Refine LS restraints |
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LS refinement shell |
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