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Yorodumi- PDB-4ym3: Crystal structure of the human galectin-4 C-terminal carbohydrate... -
+Open data
-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 | |||||||||
Components | Galectin-4 | |||||||||
Keywords | SUGAR BINDING PROTEIN / galectin / lectin / beta sandwich / carbohydrate recognition / lactose / carbohydrate 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: 1.89 Å | |||||||||
Authors | Bum-Erdene, K. / Blanchard, H. | |||||||||
Funding support | Australia, 1items
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Citation | Journal: Febs J. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ym3.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ym3.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ym3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/4ym3 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/4ym3 | HTTPS FTP |
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-Related structure data
Related structure data | 4ylzC 4ym0C 4ym1C 4ym2C 3ojbS 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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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.) 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: 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: 1.97 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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9713 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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