+Open data
-Basic information
Entry | Database: PDB / ID: 6kjy | ||||||
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Title | Galectin-13 variant C136S/C138S | ||||||
Components | Galactoside-binding soluble lectin 13 | ||||||
Keywords | SUGAR BINDING PROTEIN / Galectin-13 variant C136S/C138S | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Su, J. | ||||||
Citation | Journal: Glycobiology / Year: 2020 Title: Galectin-13/placental protein 13: redox-active disulfides as switches for regulating structure, function and cellular distribution. Authors: Yang, T. / Yao, Y. / Wang, X. / Li, Y. / Si, Y. / Li, X. / Ayala, G.J. / Wang, Y. / Mayo, K.H. / Tai, G. / Zhou, Y. / Su, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kjy.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kjy.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/6kjy ftp://data.pdbj.org/pub/pdb/validation_reports/kj/6kjy | 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: 16385.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: variant C136S/C138S / 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: 2.49 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.5 Å / Num. obs: 27251 / % possible obs: 99.6 % / Redundancy: 11.6 % / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 1260 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.499 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.02 Å2 / Biso mean: 24.4846 Å2 / Biso min: 10.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→19.499 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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