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- PDB-4ylz: 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: 4ylz | |||||||||
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Title | Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lacto-N-neotetraose (LNnT) | |||||||||
![]() | Galectin-4 | |||||||||
![]() | SUGAR BINDING PROTEIN / galectin / lectin / carbohydrate binding protein / lacto-N-neotetraose / carbohydrate recognition / beta sandwich / glycosphingolipid | |||||||||
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 | ![]() | 129.8 KB | Display | ![]() |
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PDB format | ![]() | 99.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ym0C ![]() 4ym1C ![]() 4ym2C ![]() 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 | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...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-GOL / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.33 % |
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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 | Resolution: 2.1→44.85 Å / Num. obs: 29532 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Net I/σ(I): 19.5 / Num. measured all: 164090 / Scaling rejects: 34 | |||||||||||||||||||||||||||
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→44.85 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2654 / WRfactor Rwork: 0.2055 / FOM work R set: 0.8579 / SU B: 5.992 / SU ML: 0.163 / SU R Cruickshank DPI: 0.3153 / SU Rfree: 0.2327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.233 / 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: 68.62 Å2 / Biso mean: 25.471 Å2 / Biso min: 11.92 Å2
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Refinement step | Cycle: final / Resolution: 2.1→44.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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