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Open data
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Basic information
Entry | Database: PDB / ID: 4x51 | ||||||
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Title | X-ray structure of mouse interleukin-10 mutant - S1_E8del, C149Y | ||||||
![]() | Interleukin-10 | ||||||
![]() | IMMUNE SYSTEM / cytokine / interleukin-10 family / helix bundle | ||||||
Function / homology | ![]() : / negative regulation of tumor necrosis factor production => GO:0032720 / : / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / positive regulation of cytokine production => GO:0001819 / negative regulation of myeloid dendritic cell activation / response to carbon monoxide ...: / negative regulation of tumor necrosis factor production => GO:0032720 / : / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / positive regulation of cytokine production => GO:0001819 / negative regulation of myeloid dendritic cell activation / response to carbon monoxide / positive regulation of B cell apoptotic process / negative regulation of sensory perception of pain / response to inactivity / negative regulation of membrane protein ectodomain proteolysis / : / negative regulation of heterotypic cell-cell adhesion / response to xenobiotic stimulus => GO:0009410 / negative regulation of cytokine production involved in immune response / regulation of sensory perception of pain / negative regulation of MHC class II biosynthetic process / branching involved in labyrinthine layer morphogenesis / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / negative regulation of cytokine production / cellular response to hepatocyte growth factor stimulus / regulation of synapse organization / positive regulation of sprouting angiogenesis / negative regulation of B cell proliferation / defense response to protozoan / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of endothelial cell apoptotic process / positive regulation of cell cycle / response to glucocorticoid / positive regulation of endothelial cell proliferation / negative regulation of autophagy / response to activity / cytokine activity / cellular response to estradiol stimulus / liver regeneration / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / response to molecule of bacterial origin / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / negative regulation of inflammatory response / regulation of gene expression / cellular response to lipopolysaccharide / negative regulation of neuron apoptotic process / protein dimerization activity / defense response to bacterium / immune response / negative regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuenze, G. | ||||||
![]() | ![]() Title: X-ray structure of mouse interleukin-10 mutant - S1_E8del, C149Y Authors: Kuenze, 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 | ![]() | 71.7 KB | Display | ![]() |
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PDB format | ![]() | 53.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 436.8 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lk3S S: Starting model for refinement |
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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: 19222.205 Da / Num. of mol.: 2 / Fragment: UNP residues 27-178 / Mutation: S1_E8del, C149Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.58 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Crystals grew at 20-30% (v/v) glycerolethoxylate, 0.2M ammonium acetate, 0.1M MES (pH 6.3 - 6.8). Crystals appeared after 1-2 days and reached their final size after 3-4 days. PH range: 6.3 - 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→42.15 Å / Num. obs: 17734 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LK3 Resolution: 2.05→42.15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.236 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 38.334 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→42.15 Å
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