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- PDB-2d3v: Crystal Structure of Leukocyte Ig-like Receptor A5 (LILRA5/LIR9/ILT11) -
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Open data
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Basic information
Entry | Database: PDB / ID: 2d3v | ||||||
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Title | Crystal Structure of Leukocyte Ig-like Receptor A5 (LILRA5/LIR9/ILT11) | ||||||
![]() | leukocyte immunoglobulin-like receptor subfamily A member 5 isoform 1 | ||||||
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Function / homology | ![]() positive regulation of cell activation / positive regulation of tumor necrosis factor production => GO:0032760 / negative regulation of interleukin-13 production / negative regulation of interleukin-12 production / positive regulation of calcium ion transport / positive regulation of interleukin-10 production / positive regulation of protein tyrosine kinase activity / positive regulation of interleukin-1 beta production / positive regulation of inflammatory response / positive regulation of interleukin-6 production ...positive regulation of cell activation / positive regulation of tumor necrosis factor production => GO:0032760 / negative regulation of interleukin-13 production / negative regulation of interleukin-12 production / positive regulation of calcium ion transport / positive regulation of interleukin-10 production / positive regulation of protein tyrosine kinase activity / positive regulation of interleukin-1 beta production / positive regulation of inflammatory response / positive regulation of interleukin-6 production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of MAPK cascade / membrane => GO:0016020 / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shiroishi, M. / Kajikawa, M. / Kuroki, K. / Ose, T. / Kohda, D. / Maenaka, K. | ||||||
![]() | ![]() Title: Crystal structure of the human monocyte-activating receptor, Authors: Shiroishi, M. / Kajikawa, M. / Kuroki, K. / Ose, T. / Kohda, D. / Maenaka, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.9 KB | Display | ![]() |
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PDB format | ![]() | 36.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22123.561 Da / Num. of mol.: 1 / Fragment: Extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 49.6 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Bicine, PEG20000, Dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 19328 / % possible obs: 92.1 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.6 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1011 / % possible all: 49.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The structure was refined also with CNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.844 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.848→1.896 Å / Total num. of bins used: 20
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