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- PDB-6grs: Paired immunoglobulin-like receptor B (PirB) or Leukocyte immunog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6grs | |||||||||
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Title | Paired immunoglobulin-like receptor B (PirB) or Leukocyte immunoglobulin-like receptor subfamily B member 3 (LILRB3) full extracellular domain | |||||||||
![]() | Paired immunoglobulin-like receptor B | |||||||||
![]() | IMMUNE SYSTEM / neuronal growth inhibition / B cell down regulation | |||||||||
Function / homology | ![]() inhibitory MHC class I receptor activity / cytokine-mediated signaling pathway / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vlieg, H.C. / Huizinga, E.G. / Janssen, B.J.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and flexibility of the extracellular region of the PirB receptor. Authors: Vlieg, H.C. / Huizinga, E.G. / Janssen, B.J.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.7 KB | Display | ![]() |
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PDB format | ![]() | 193.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6grqC ![]() 6grtC ![]() 2d3vS ![]() 4llaS S: Starting model for refinement C: citing same article ( |
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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: 67456.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.69 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.2 M LiCl, 12% PEG 6000m 0.1 M Citric acid buffer pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→52.69 Å / Num. obs: 25778 / % possible obs: 98.8 % / Redundancy: 3.2 % / CC1/2: 0.949 / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3.4→3.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4683 / CC1/2: 0.586 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2D3V, 4LLA Resolution: 3.4→52.686 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→52.686 Å
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Refine LS restraints |
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LS refinement shell |
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