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- PDB-3ap4: Crystal structure of the galectin-8 N-terminal carbohydrate recog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ap4 | |||||||||
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Title | Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose | |||||||||
![]() | Galectin-8![]() | |||||||||
![]() | SUGAR BINDING PROTEIN / ![]() ![]() | |||||||||
Function / homology | ![]() lymphatic endothelial cell migration / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Matsuzaka, T. / Ideo, H. / Yamashita, K. / Nonaka, T. | |||||||||
![]() | ![]() Title: Galectin-8-N-domain recognition mechanism for sialylated and sulfated glycans Authors: Ideo, H. / Matsuzaka, T. / Nonaka, T. / Seko, A. / Yamashita, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.1 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 17423.123 Da / Num. of mol.: 4 / Fragment: N-terminal carbohydrate recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Polysaccharide | beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose #3: Water | ChemComp-HOH / | ![]() Sequence details | THIS RESIDUE IS CAUSED BY NATURAL VARIANT. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 3, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.33→59.462 Å / Num. all: 26924 / Num. obs: 26924 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 23.253 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 |
Reflection shell | Resolution: 2.33→2.39 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 10.7 / Num. unique all: 1581 / Rsym value: 0.06 / % possible all: 76.3 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.209 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→51.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.39 Å / Total num. of bins used: 20
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