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- PDB-4ym3: 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: 4ym3 | |||||||||
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Title | Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lactose | |||||||||
![]() | Galectin-4 | |||||||||
![]() | SUGAR BINDING PROTEIN / galectin / lectin / beta sandwich / carbohydrate recognition / lactose / carbohydrate binding protein | |||||||||
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 | ![]() | 130.4 KB | Display | ![]() |
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PDB format | ![]() | 99.6 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 | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ylzC ![]() 4ym0C ![]() 4ym1C ![]() 4ym2C ![]() 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 | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.61 % |
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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 pH 7.0, 4 % v/v PEG 400 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9713 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.889→65.092 Å / Num. all: 41495 / Num. obs: 41495 / % possible obs: 98.9 % / Redundancy: 12.1 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.202 / Rsym value: 0.195 / Net I/av σ(I): 2.164 / Net I/σ(I): 15.8 / Num. measured all: 500962 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3OJB Resolution: 1.89→45.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.1985 / WRfactor Rwork: 0.1719 / FOM work R set: 0.8342 / SU B: 2.828 / SU ML: 0.09 / SU R Cruickshank DPI: 0.0333 / SU Rfree: 0.0279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.028 / 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: 49.57 Å2 / Biso mean: 20.778 Å2 / Biso min: 9.19 Å2
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Refinement step | Cycle: final / Resolution: 1.89→45.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.889→1.938 Å / Total num. of bins used: 20
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