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- PDB-4j6j: Crystal structure of calcium2+-free wild-type CD23 lectin domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j6j | ||||||
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Title | Crystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form A) | ||||||
![]() | Low affinity immunoglobulin epsilon Fc receptor | ||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dhaliwal, B. / Yahya, N. / Sutton, B.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.8 KB | Display | ![]() |
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PDB format | ![]() | 187.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4j6kC ![]() 4j6lC ![]() 4j6mC ![]() 4j6nC ![]() 4j6pC ![]() 4j6qC ![]() 4g96S 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16164.986 Da / Num. of mol.: 4 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.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.25 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 16 % (w/v) PEG 6,000, 2 % (v/v) 1,6-hexanediol, 0.05 M ammonium sulfate and 0.1 M sodium acetate pH 4.7 , VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→57.96 Å / Num. all: 50712 / Num. obs: 48544 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Limit h max: 27 / Limit h min: -27 / Limit k max: 29 / Limit k min: -27 / Limit l max: 32 / Limit l min: 0 |
Reflection shell | % possible obs: 96.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.73 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4G96 Resolution: 1.9→15.57 Å / Cor.coef. Fo:Fc: 0.9485 / Cor.coef. Fo:Fc free: 0.9344 / Occupancy max: 1 / Occupancy min: 0.25 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 224.75 Å2 / Biso mean: 40.9941 Å2 / Biso min: 13.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.268 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→15.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 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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