[English] 日本語
Yorodumi- PDB-3zsm: Crystal structure of Apo Human Galectin-3 CRD at 1.25 angstrom re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zsm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Apo Human Galectin-3 CRD at 1.25 angstrom resolution, at room temperature | ||||||
Components | GALECTIN-3 | ||||||
Keywords | SUGAR BINDING PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / negative regulation of endocytosis / IgE binding / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / negative regulation of endocytosis / IgE binding / positive regulation of mononuclear cell migration / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / regulation of T cell proliferation / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / RNA splicing / neutrophil chemotaxis / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Saraboji, K. / Hakansson, M. / Diehl, C. / Nilsson, U.J. / Leffler, H. / Akke, M. / Logan, D.T. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: The Carbohydrate-Binding Site in Galectin-3 is Pre-Organized to Recognize a Sugar-Like Framework of Oxygens: Ultra-High Resolution Structures and Water Dynamics. Authors: Saraboji, K. / Hakansson, M. / Genheden, S. / Diehl, C. / Qvist, J. / Weininger, U. / Nilsson, U.J. / Leffler, H. / Ryde, U. / Akke, M. / Logan, D.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zsm.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zsm.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zsm_validation.pdf.gz | 415.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3zsm_full_validation.pdf.gz | 417.8 KB | Display | |
Data in XML | 3zsm_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 3zsm_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/3zsm ftp://data.pdbj.org/pub/pdb/validation_reports/zs/3zsm | HTTPS FTP |
-Related structure data
Related structure data | 3zsjSC 3zskC 3zslC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15735.129 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 114-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17931 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.9 % Description: STRUCTURE SOLVED BY STANDARD RIGID-BODY REFINEMENT USING REFMAC5 |
---|---|
Crystal grow | pH: 7.5 Details: 30% PEG 4000, 0.1M MGCL2, 0.008M BETA MERCAPTOETHANOL, 0.1M TRIS-HCL, PH 7.5, 0.4M NASCN |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90778 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 29, 2009 |
Radiation | Monochromator: BENT SI (220) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90778 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→30 Å / Num. obs: 37798 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.5 / % possible all: 97.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZSJ Resolution: 1.25→30 Å / Num. parameters: 12543 / Num. restraintsaints: 16351 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 29 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1266.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→30 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|