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Open data
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Basic information
Entry | Database: PDB / ID: 4mxv | ||||||
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Title | Structure of Lymphotoxin alpha bound to anti-LTa Fab | ||||||
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![]() | CYTOKINE/IMMUNE SYSTEM / TNF / Tumor Necrosis Factor / TNFR Receptor / lymphotoxin beta receptor / lymphotoxin alpha / Lymphoid development / Tumor immunity / Auto-immunity / CYTOKINE-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of humoral immune response mediated by circulating immunoglobulin / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / tumor necrosis factor receptor binding / humoral immune response / lymph node development / negative regulation of fibroblast proliferation / positive regulation of glial cell proliferation / response to nutrient ...positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of humoral immune response mediated by circulating immunoglobulin / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / tumor necrosis factor receptor binding / humoral immune response / lymph node development / negative regulation of fibroblast proliferation / positive regulation of glial cell proliferation / response to nutrient / cytokine activity / TNFR2 non-canonical NF-kB pathway / positive regulation of type II interferon production / cell-cell signaling / response to lipopolysaccharide / response to hypoxia / defense response to Gram-positive bacterium / response to xenobiotic stimulus / positive regulation of apoptotic process / signaling receptor binding / apoptotic process / signal transduction / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yin, J.P. / Hymowitz, S.G. | ||||||
![]() | ![]() Title: Dimerization of LT beta R by LT alpha 1 beta 2 is necessary and sufficient for signal transduction. Authors: Sudhamsu, J. / Yin, J. / Chiang, E.Y. / Starovasnik, M.A. / Grogan, J.L. / Hymowitz, S.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 322.9 KB | Display | ![]() |
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PDB format | ![]() | 264.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.3 KB | Display | ![]() |
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Full document | ![]() | 509.6 KB | Display | |
Data in XML | ![]() | 56.2 KB | Display | |
Data in CIF | ![]() | 77.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mxwC ![]() 1fveS ![]() 1tnrS 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: 17313.338 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23065.541 Da / Num. of mol.: 3 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 22890.713 Da / Num. of mol.: 3 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 12% PEG6000, 2 M sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2007 | |||||||||||||||||||||
Radiation | Monochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. all: 46756 / Num. obs: 46756 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1TNR AND 1FVE Resolution: 3.2→29.796 Å / SU ML: 0.37 / σ(F): 2 / Phase error: 20.96 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→29.796 Å
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Refine LS restraints |
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LS refinement shell |
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