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Yorodumi- PDB-5duv: Crystal structure of the human galectin-4 N-terminal carbohydrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5duv | |||||||||
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Title | Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with lactose | |||||||||
Components | Galectin-4 | |||||||||
Keywords | SUGAR BINDING PROTEIN / galectin-4 / lectin / lactose / sugar-binding protein | |||||||||
Function / homology | Function and homology information antibacterial peptide biosynthetic process / galactoside binding / carbohydrate binding / collagen-containing extracellular matrix / cell adhesion / extracellular space / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Bum-Erdene, K. / Blanchard, H. | |||||||||
Funding support | Australia, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: Structural characterisation of human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol, lactose, 3'-sulfo-lactose, and 2'-fucosyllactose. Authors: Bum-Erdene, K. / Leffler, H. / Nilsson, U.J. / Blanchard, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5duv.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5duv.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 5duv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/5duv ftp://data.pdbj.org/pub/pdb/validation_reports/du/5duv | HTTPS FTP |
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-Related structure data
Related structure data | 5duuC 5duwC 5duxC 3i8tS 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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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: 17473.912 Da / Num. of mol.: 4 Fragment: N-terminal carbohydrate recognition domain (UNP residues 1-155) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS4 / Production host: Escherichia coli (E. coli) / References: UniProt: P56470 #2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.2 M calcium acetate, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→37.24 Å / Num. obs: 40168 / % possible obs: 98.1 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.044 / Net I/σ(I): 12.2 / Num. measured all: 161697 / Scaling rejects: 168 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I8T Resolution: 1.9→37.24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1926 / WRfactor Rwork: 0.1506 / FOM work R set: 0.8706 / SU B: 3.264 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1577 / SU Rfree: 0.1396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.14 / 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: 76.66 Å2 / Biso mean: 17.307 Å2 / Biso min: 5.29 Å2
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Refinement step | Cycle: final / Resolution: 1.9→37.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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