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- PDB-4ym2: Crystal structure of the human galectin-4 C-terminal carbohydrate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ym2 | |||||||||
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Title | Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lactose-3'-sulfate | |||||||||
![]() | Galectin-4 | |||||||||
![]() | SUGAR BINDING PROTEIN / galectin / lectin / carbohydrate binding protein / sulfated saccharide / carbohydrate recognition / beta sandwich | |||||||||
Function / homology | ![]() antibacterial peptide biosynthetic process / galactoside binding / carbohydrate binding / collagen-containing extracellular matrix / cell adhesion / extracellular space / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bum-Erdene, K. / Blanchard, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of human galectin-4 C-terminal domain: elucidating the molecular basis for recognition of glycosphingolipids, sulfated saccharides and blood group antigens. Authors: Bum-Erdene, K. / Leffler, H. / Nilsson, U.J. / Blanchard, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.3 KB | Display | ![]() |
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PDB format | ![]() | 96.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ylzC ![]() 4ym0C ![]() 4ym1C ![]() 4ym3C ![]() 3ojbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 16962.291 Da / Num. of mol.: 4 / Fragment: unp residues 171-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | #3: Polysaccharide | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 36.39 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2 M ammonium sulfate, 0.1 M HEPES, 4 % v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→44.91 Å / Num. obs: 29564 / % possible obs: 98.4 % / Redundancy: 5.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.045 / Net I/σ(I): 12.5 / Num. measured all: 161411 / Scaling rejects: 12 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3OJB Resolution: 2.1→42.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2219 / WRfactor Rwork: 0.1675 / FOM work R set: 0.8503 / SU B: 4.736 / SU ML: 0.128 / SU R Cruickshank DPI: 0.0502 / SU Rfree: 0.0387 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.57 Å2 / Biso mean: 28.064 Å2 / Biso min: 7.61 Å2
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Refinement step | Cycle: final / Resolution: 2.1→42.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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