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- PDB-6grq: 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: 6grq | |||||||||
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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 | ![]() | 236.3 KB | Display | ![]() |
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PDB format | ![]() | 189.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 712.6 KB | Display | ![]() |
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Full document | ![]() | 719.7 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6grsC ![]() 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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#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 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.09 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.1 M LiCL, 14% PEG 6000, 0.1M citic 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: Oct 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→53.19 Å / Num. obs: 19634 / % possible obs: 100 % / Redundancy: 22.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.277 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.3→3.56 Å / Redundancy: 22.5 % / Rmerge(I) obs: 2.767 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3949 / CC1/2: 0.542 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2D3V, 4LLA Resolution: 3.3→53.188 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 34.79 / 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: 3.3→53.188 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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