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Yorodumi- PDB-7xxv: Macaca fascicularis galectin-10/Charcot-Leyden crystal protein wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xxv | ||||||
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Title | Macaca fascicularis galectin-10/Charcot-Leyden crystal protein with lactose | ||||||
Components | Galectin | ||||||
Keywords | SURFACTANT PROTEIN / Macaca fascicularis galectin-10/Charcot-Leyden crystal protein with lactose | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Macaca fascicularis (crab-eating macaque) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Su, J.Y. | ||||||
Funding support | 1items
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Citation | Journal: Acta Biochim.Biophys.Sin. / Year: 2023 Title: Glutathione disrupts galectin-10 Charcot-Leyden crystal formation to possibly ameliorate eosinophil-based diseases such as asthma. Authors: Na, H. / Sayed, H. / Ayala, G.J. / Wang, X. / Liu, Y. / Yu, J. / Liu, T. / Mayo, K.H. / Su, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xxv.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xxv.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xxv_validation.pdf.gz | 803.9 KB | Display | wwPDB validaton report |
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Full document | 7xxv_full_validation.pdf.gz | 804.2 KB | Display | |
Data in XML | 7xxv_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 7xxv_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/7xxv ftp://data.pdbj.org/pub/pdb/validation_reports/xx/7xxv | HTTPS FTP |
-Related structure data
Related structure data | 7xxuC 7xxwC 7xxxC 7xxyC 7xxzC 5xrgS S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16198.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca fascicularis (crab-eating macaque) Gene: EGM_09723 / Production host: Escherichia coli (E. coli) / References: UniProt: G7PXK5 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.97 Å / Num. obs: 24980 / % possible obs: 99.7 % / Redundancy: 17.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.768 / Num. unique obs: 1152 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XRG Resolution: 1.6→19.97 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.32 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.9 Å2 / Biso mean: 18.52 Å2 / Biso min: 8.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→19.97 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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