+Open data
-Basic information
Entry | Database: PDB / ID: 5y03 | ||||||
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Title | Galectin-13/Placental Protein 13 variant R53H crystal structure | ||||||
Components | Galactoside-binding soluble lectin 13 | ||||||
Keywords | SUGAR BINDING PROTEIN / Galectin-13/Placental Protein 13 | ||||||
Function / homology | Function and homology information lysophospholipase activity / phospholipid metabolic process / nuclear matrix / carbohydrate binding / nuclear body / apoptotic process / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.12 Å | ||||||
Authors | Wang, Y. / Su, J. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Galectin-13, a different prototype galectin, does not bind beta-galacto-sides and forms dimers via intermolecular disulfide bridges between Cys-136 and Cys-138. Authors: Su, J. / Wang, Y. / Si, Y. / Gao, J. / Song, C. / Cui, L. / Wu, R. / Tai, G. / Zhou, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y03.cif.gz | 39.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y03.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/5y03 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/5y03 | HTTPS FTP |
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-Related structure data
-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: 16398.750 Da / Num. of mol.: 1 / Mutation: R53H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS13, PLAC8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHV8 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→19.052 Å / Num. obs: 7985 / % possible obs: 99.8 % / Redundancy: 1.9 % / Net I/σ(I): 6.6 |
-Processing
Software |
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Refinement | Resolution: 2.12→19.05 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 27.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 71.61 Å2 / Biso mean: 33.4555 Å2 / Biso min: 19.78 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.12→19.05 Å
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