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Open data
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Basic information
Entry | Database: PDB / ID: 8p8s | |||||||||
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Title | Recombinant Ym2 crystal structure | |||||||||
![]() | Chitinase-like protein 4 | |||||||||
![]() | IMMUNE SYSTEM / Ym2 / Chil4 / in vivo crystallization / chitinase-like protein | |||||||||
Function / homology | ![]() production of molecular mediator involved in inflammatory response / chitin catabolic process / chitin binding / positive regulation of chemokine production / kinase binding / carbohydrate metabolic process / extracellular space / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Verschueren, K.H.G. / Verstraete, K. / Heyndrickx, I. / Smole, U. / Aegerter, A. / Savvides, S.N. / Lambrecht, B.N. | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Ym1 protein crystals promote type 2 immunity. Authors: Heyndrickx, I. / Deswarte, K. / Verstraete, K. / Verschueren, K.H.G. / Smole, U. / Aegerter, H. / Dansercoer, A. / Hammad, H. / Savvides, S.N. / Lambrecht, B.N. #1: ![]() Title: Ym1 protein crystals promote type 2 immunity Authors: Heyndrickx, I. / Deswarte, K. / Verstraete, K. / Verschueren, K. / Smole, U. / Aegerter, H. / Dansercoer, A. / Hammad, H. / Savvides, S. / Lambrecht, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.8 KB | Display | ![]() |
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PDB format | ![]() | 236 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.7 KB | Display | ![]() |
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Full document | ![]() | 436.7 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p8qC ![]() 8p8rC ![]() 8p8tC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 47413.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The cDNA sequence encoding murine Ym2 (Uniprot Q91Z98, residues 22 - 402) was cloned in the pTwist-CMV-BetaGlobin mammalian expression vector, in frame with the mouse IgH signal peptide ...Details: The cDNA sequence encoding murine Ym2 (Uniprot Q91Z98, residues 22 - 402) was cloned in the pTwist-CMV-BetaGlobin mammalian expression vector, in frame with the mouse IgH signal peptide (MGWSCIIFFLVATATGVHS), and an N-terminal hexahistine-tag followed by a Tobacco Etch Virus (TEV)-protease cleavage site. Ym2 was purified via IMAC and SEC. Before crystallization the His-tag was removed by incubation with TEV protease. Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M sodium acetate pH 6.0 and 200 mM CaCl / Temp details: Temperature controlled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cold N2 gas stream / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2019 |
Radiation | Monochromator: 0.9763 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→59.73 Å / Num. obs: 119183 / % possible obs: 98.4 % / Redundancy: 6.76 % / Biso Wilson estimate: 12.048 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.08 / Net I/σ(I): 15.12 |
Reflection shell | Resolution: 1.17→1.24 Å / Mean I/σ(I) obs: 4.74 / Num. unique obs: 18719 / CC1/2: 0.925 / Rrim(I) all: 0.358 / % possible all: 95.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 11.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.12 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.17→37.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.17→1.18 Å / Total num. of bins used: 50
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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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