+Open data
-Basic information
Entry | Database: PDB / ID: 6a65 | ||||||
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Title | Placental protein 13/galectin-13 variant R53HR55N with Tris | ||||||
Components | Galactoside-binding soluble lectin 13 | ||||||
Keywords | SUGAR BINDING PROTEIN | ||||||
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: 1.771 Å | ||||||
Authors | Su, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Biosci. Rep. / Year: 2018 Title: Resetting the ligand binding site of placental protein 13/galectin-13 recovers its ability to bind lactose Authors: Su, J. / Cui, L. / Si, Y. / Song, C. / Li, Y. / Yang, T. / Wang, H. / Mayo, K.H. / 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 | 6a65.cif.gz | 39.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a65.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 6a65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/6a65 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/6a65 | 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
#1: Protein | Mass: 15942.188 Da / Num. of mol.: 1 / Fragment: UNP residues 2-139 / Mutation: R53H, R55N 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: Chemical | ChemComp-TRS / |
#3: 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: 2.07 Å3/Da / Density % sol: 40.71 % |
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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: 0.977 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→18.911 Å / Num. obs: 13108 / % possible obs: 98.7 % / Redundancy: 1 % / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.77→1.81 Å |
-Processing
Software | Name: PHENIX / Version: (1.10.1_2155: ???) / Classification: refinement | ||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.771→18.911 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 70.14 Å2 / Biso mean: 35.5917 Å2 / Biso min: 24.3 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.771→18.911 Å
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