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- PDB-7l66: C-type carbohydrate-recognition domain 4 of the mannose receptor ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l66 | ||||||
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Title | C-type carbohydrate-recognition domain 4 of the mannose receptor complexed with Methyl-GlcNAc | ||||||
![]() | Macrophage mannose receptor 1 | ||||||
![]() | SUGAR BINDING PROTEIN / GLYCOBIOLOGY / CARBOHYDRATE-BINDING PROTEIN / C-TYPE LECTIN / COMPLEX | ||||||
Function / homology | ![]() cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity ...cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weis, W.I. / Feinberg, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of carbohydrate binding by the macrophage mannose receptor CD206. Authors: Feinberg, H. / Jegouzo, S.A.F. / Lasanajak, Y. / Smith, D.F. / Drickamer, K. / Weis, W.I. / Taylor, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.7 KB | Display | ![]() |
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PDB format | ![]() | 50.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jubSC ![]() 7jucC ![]() 7judC ![]() 7jueC ![]() 7jufC ![]() 7jugC ![]() 7juhC ![]() 7l61C ![]() 7l62C ![]() 7l63C ![]() 7l64C ![]() 7l65C ![]() 7l67C ![]() 7l68C 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: 15493.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Sugar | ChemComp-2F8 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.03 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Protein solution: 3mg/ml protein in 5 mM CaCl2, 10 mM Tris, pH 8.0, 25 mM NaCl, and 50mM alpha-Me-GlcNAc. Reservoir solution: 20% Peg 8K, 0.1M MES, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→34.44 Å / Num. obs: 13185 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.021 / Rrim(I) all: 0.075 / Net I/σ(I): 20.2 / Num. measured all: 173468 / Scaling rejects: 314 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JUB Resolution: 1.75→34.44 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / Phase error: 22.21 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.18 Å2 / Biso mean: 31.5273 Å2 / Biso min: 12.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→34.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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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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