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Yorodumi- PDB-3ap9: Crystal structure of the galectin-8 N-terminal carbohydrate recog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ap9 | |||||||||
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Title | Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with Lacto-N-fucopentaose III | |||||||||
Components | Galectin-8 | |||||||||
Keywords | SUGAR BINDING PROTEIN / Beta-Sandwich / Galectin / Carbohydrate/Sugar Binding / Lacto-N-fucopentaose III | |||||||||
Function / homology | Function and homology information lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / extracellular space / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | |||||||||
Authors | Matsuzaka, T. / Ideo, H. / Yamashita, K. / Nonaka, T. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ap9.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ap9.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ap9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ap9_validation.pdf.gz | 750.4 KB | Display | wwPDB validaton report |
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Full document | 3ap9_full_validation.pdf.gz | 752.4 KB | Display | |
Data in XML | 3ap9_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3ap9_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/3ap9 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/3ap9 | HTTPS FTP |
-Related structure data
Related structure data | 3ap4C 3ap5SC 3ap6C 3ap7C C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 17423.123 Da / Num. of mol.: 1 / Fragment: N-terminal carbohydrate recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214 | ||||
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#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | ChemComp-MPD / ( | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THIS RESIDUE IS CAUSED BY NATURAL VARIANT. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.34 % |
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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 Lacto-N-fucopentaose III, 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: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2006 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→24.977 Å / Num. all: 37685 / Num. obs: 37685 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 9.616 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 |
Reflection shell | Resolution: 1.33→1.36 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 9.4 / Num. unique all: 2712 / Rsym value: 0.231 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AP5 Resolution: 1.33→24.977 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.648 / SU ML: 0.028 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 8.336 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→24.977 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.33→1.364 Å / Total num. of bins used: 20
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