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Open data
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Basic information
Entry | Database: PDB / ID: 7cyb | ||||||
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Title | Saimiri boliviensis boliviensis galectin-13 with glycerol | ||||||
![]() | Galectin![]() | ||||||
![]() | SUGAR BINDING PROTEIN / Saimiri boliviensis boliviensis galectin-13 with glycerol | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Su, J. | ||||||
![]() | ![]() Title: Actin binding to galectin-13/placental protein-13 occurs independently of the galectin canonical ligand-binding site. Authors: Li, X. / Yao, Y. / Liu, T. / Gu, K. / Han, Q. / Zhang, W. / Ayala, G.J. / Liu, Y. / Na, H. / Yu, J. / Zhang, F. / Mayo, K.H. / Su, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.4 KB | Display | ![]() |
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PDB format | ![]() | 77.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cyaC ![]() 6kjxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 16488.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() | ||||
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#2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.85 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→19.82 Å / Num. obs: 18965 / % possible obs: 98.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.099 / Num. unique obs: 929 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6KJX Resolution: 1.6→19.82 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.89 / 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: 69.84 Å2 / Biso mean: 19.3176 Å2 / Biso min: 6.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→19.82 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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