+Open data
-Basic information
Entry | Database: PDB / ID: 8p8t | |||||||||
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Title | Ex vivo Ym2 crystal structure | |||||||||
Components | Chitinase-like protein 4 | |||||||||
Keywords | IMMUNE SYSTEM / Ym2 / Chil4 / in vivo crystallization / chitinase-like protein | |||||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | |||||||||
Authors | Verschueren, K.H.G. / Verstraete, K. / Heyndrickx, I. / Smole, U. / Aegerter, H. / Savvides, S.N. / Lambrecht, B.N. | |||||||||
Funding support | European Union, Belgium, 2items
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Citation | Journal: Elife / Year: 2024 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: Journal: Elife / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p8t.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p8t.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 8p8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p8t_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 8p8t_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 8p8t_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 8p8t_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/8p8t ftp://data.pdbj.org/pub/pdb/validation_reports/p8/8p8t | HTTPS FTP |
-Related structure data
Related structure data | 8p8qC 8p8rC 8p8sC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45020.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Single ex vivo Ym2 crystals were harvested from the BAL fluid of C57BL/6J-Tg(CAG-Gal10)Bla mice. The sequence corresponds to Uniprot ID Q91Z98. Source: (natural) Mus musculus (house mouse) / Organ: Lung / Plasmid details: BAL fluid / Strain: C57BL/6J-Tg(CAG-Gal10)Bla / References: UniProt: Q91Z98 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.2 % / Description: Plate-like crystals |
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Crystal grow | Temperature: 310 K / Method: in cell Details: Single ex vivo Ym2 crystals were harvested from the BAL fluid of transgenic C57BL/6J-Tg(CAG-Gal10)Bla mice and cryoprotected by a brief soak in PBS + 35% (v/v) glycerol. Temp details: In vivo (mouse) crystallisation |
-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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0000089224 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0000089224 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→60.01 Å / Num. obs: 39074 / % possible obs: 97.7 % / Redundancy: 3.47 % / Biso Wilson estimate: 24.584 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.177 / Net I/σ(I): 6.59 |
Reflection shell | Resolution: 1.7→1.81 Å / Mean I/σ(I) obs: 0.96 / Num. unique obs: 6228 / CC1/2: 0.358 / Rrim(I) all: 1.364 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→16.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.102
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Displacement parameters | Biso mean: 19.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.71→16.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.72 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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