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Yorodumi- PDB-3zhg: Crystallographic structure of the native mouse SIGN-R1 CRD domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zhg | ||||||
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Title | Crystallographic structure of the native mouse SIGN-R1 CRD domain | ||||||
Components | (CD209 ANTIGEN-LIKE PROTEIN B) x 2 | ||||||
Keywords | IMMUNE SYSTEM / C-LECTIN CRD / CAPSULAR POLYSACCHARIDE. | ||||||
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: 1.87 Å | ||||||
Authors | Silva-Martin, N. / Bartual, S.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. / Ramirez-Aportela, E. / Chacon, P. / 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 | 3zhg.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zhg.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zhg ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zhg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 17973.301 Da / Num. of mol.: 3 / Fragment: CRD, RESIDUES 191-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) Cell line (production host): CHINESE HAMSTER OVARY (CHO) CELLS Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY / References: UniProt: Q8CJ91 #2: Protein | | Mass: 18001.314 Da / Num. of mol.: 1 / Fragment: CRD RESIDUES 190-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) Cell line (production host): CHINESE HAMSTER OVARY (CHO) CELLS Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY / References: UniProt: Q8CJ91 #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CA / #5: 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: 3.17 Å3/Da / Density % sol: 61.19 % / Description: NONE |
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Crystal grow | Details: CRYSTALS GROWN BY MIXING 1 UL OF CRD_SIGN-R1 (4 MG/ML IN 20 MM TRIS/HCL PH 7.5 AND 100 MM NACL) WITH 1UL OF PRECIPITANT CONSISTING IN 0.1 M BISTRIS PH 5.5 AND 1.6 M (NH4)2SO4. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07225 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→74.53 Å / Num. obs: 52474 / % possible obs: 93 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.87→1.98 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→27.627 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 30.81 / 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 / Bsol: 33.747 Å2 / ksol: 0.364 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.87→27.627 Å
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Refine LS restraints |
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LS refinement shell |
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