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Yorodumi- PDB-4j6m: Crystal structure of calcium2+-free wild-type CD23 lectin domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j6m | ||||||
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Title | Crystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form D) | ||||||
Components | Low affinity immunoglobulin epsilon Fc receptor | ||||||
Keywords | IMMUNE SYSTEM / immunoglobulin fold lectin / antibody receptor | ||||||
Function / homology | Function and homology information low-affinity IgE receptor activity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / macrophage activation / IgE binding / positive regulation of killing of cells of another organism / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling ...low-affinity IgE receptor activity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / macrophage activation / IgE binding / positive regulation of killing of cells of another organism / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling / positive regulation of nitric-oxide synthase activity / integrin binding / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / immune response / external side of plasma membrane / extracellular exosome / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å | ||||||
Authors | Dhaliwal, B. / Fabiane, S.M. / Sutton, B.J. | ||||||
Citation | Journal: Mol.Immunol. / Year: 2013 Title: Conformational plasticity at the IgE-binding site of the B-cell receptor CD23. Authors: Dhaliwal, B. / Pang, M.O. / Yuan, D. / Yahya, N. / Fabiane, S.M. / McDonnell, J.M. / Gould, H.J. / Beavil, A.J. / Sutton, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j6m.cif.gz | 429.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j6m.ent.gz | 356 KB | Display | PDB format |
PDBx/mmJSON format | 4j6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/4j6m ftp://data.pdbj.org/pub/pdb/validation_reports/j6/4j6m | HTTPS FTP |
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-Related structure data
Related structure data | 4j6jC 4j6kC 4j6lC 4j6nC 4j6pC 4j6qC 4g96S 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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Unit cell |
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-Components
#1: Protein | Mass: 16164.986 Da / Num. of mol.: 8 Fragment: Soluble head domain of the B-cell receptor CD23 (UNP Residues 156-298) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD23A, CLEC4J, FCE2, FCER2, IGEBF / Production host: Escherichia coli (E. coli) / References: UniProt: P06734 #2: Chemical | ChemComp-SO4 / #3: 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: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 22.5 % (w/v) PEG 3,350, 0.2 M ammonium sulfate and 0.1 M MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9745 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9745 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. all: 47011 / Num. obs: 46992 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.48→2.57 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2.04 / % possible all: 74.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4G96 Resolution: 2.48→36.31 Å / Cor.coef. Fo:Fc: 0.8854 / Cor.coef. Fo:Fc free: 0.8483 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.451 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 120.84 Å2 / Biso mean: 31.648 Å2 / Biso min: 4.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→36.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.48→2.54 Å / Total num. of bins used: 20
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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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