+Open data
-Basic information
Entry | Database: PDB / ID: 4c9f | |||||||||
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Title | Structure of SIGN-R1 in complex with Sulfodextran | |||||||||
Components | CD209 ANTIGEN-LIKE PROTEIN B | |||||||||
Keywords | MEMBRANE PROTEIN / C-TYPE LECTIN / INNATE IMMUNITY | |||||||||
Function / homology | Function and homology information detection of yeast / (1->3)-beta-D-glucan binding / fucose binding / phagocytosis, recognition / polysaccharide binding / D-mannose binding / detection of bacterium / positive regulation of phagocytosis / endocytosis / positive regulation of tumor necrosis factor production ...detection of yeast / (1->3)-beta-D-glucan binding / fucose binding / phagocytosis, recognition / polysaccharide binding / D-mannose binding / detection of bacterium / positive regulation of phagocytosis / endocytosis / positive regulation of tumor necrosis factor production / immune response / external side of plasma membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Silva-Martin, N. / Bartual, S.G. / Rodriguez, A. / Ramirez, E. / Chacon, P. / Anthony, R.M. / Park, C.G. / Hermoso, J.A. | |||||||||
Citation | Journal: Structure / Year: 2014 Title: Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor Sign-R1 Authors: Silva-Martin, N. / Bartual, S.G. / Rodriguez, A. / Ramirez, E. / Chacon, P. / Anthony, R.M. / Park, C.G. / Hermoso, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c9f.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c9f.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 4c9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/4c9f ftp://data.pdbj.org/pub/pdb/validation_reports/c9/4c9f | HTTPS FTP |
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-Related structure data
Related structure data | 3zhgSC 4cajC 4cdhC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 15524.574 Da / Num. of mol.: 4 / Fragment: CRD, RESIDUES 191-323 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: MACROPHAGES / References: UniProt: Q8CJ91 |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-4-O-sulfo-alpha- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-4-O-sulfo-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Non-polymers , 3 types, 178 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 66.38 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9334 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→61.8 Å / Num. obs: 30140 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.58→2.98 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.8 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZHG Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.36 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 34.518 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→40 Å
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Refine LS restraints |
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