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- PDB-3zsk: Crystal structure of Human Galectin-3 CRD with glycerol bound at ... -

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Basic information

Entry
Database: PDB / ID: 3zsk
TitleCrystal structure of Human Galectin-3 CRD with glycerol bound at 0.90 angstrom resolution
ComponentsGALECTIN-3
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


: / negative regulation of NK T cell activation / mononuclear cell migration / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration ...: / negative regulation of NK T cell activation / mononuclear cell migration / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / signaling receptor inhibitor activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / macrophage chemotaxis / chemoattractant activity / positive regulation of calcium ion import / monocyte chemotaxis / regulation of T cell proliferation / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / positive regulation of protein-containing complex assembly / spliceosomal complex / molecular condensate scaffold activity / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsSaraboji, K. / Hakansson, M. / Diehl, C. / Nilsson, U.J. / Leffler, H. / Akke, M. / Logan, D.T.
CitationJournal: 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
DepositionJun 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Other
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GALECTIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9193
Polymers15,7351
Non-polymers1842
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.830, 58.200, 62.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GALECTIN-3 / GAL-3 / 35 KDA LECTIN / CARBOHYDRATE-BINDING PROTEIN 35 / CBP 35 / GALACTOSE-SPECIFIC LECTIN 3 / ...GAL-3 / 35 KDA LECTIN / CARBOHYDRATE-BINDING PROTEIN 35 / CBP 35 / GALACTOSE-SPECIFIC LECTIN 3 / GALACTOSIDE-BINDING PROTEIN / GALBP / IGE-BINDING PROTEIN / L-31 / LAMININ-BINDING PROTEIN / LECTIN L-29 / MAC-2 ANTIGEN


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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.4 %
Description: STRUCTURE SOLVED BY STANDARD RIGID-BODY REFINEMENT USING REFMAC5
Crystal growpH: 7.5
Details: 30% PEG 4000, 0.1M MGCL2, 0.008M BETA MERCAPTOETHANOL, 0.1M TRIS-HCL, PH 7.5, 0.4M NASCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90778
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2009
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90778 Å / Relative weight: 1
ReflectionResolution: 0.9→20 Å / Num. obs: 93342 / % possible obs: 95.8 % / Observed criterion σ(I): 1 / Redundancy: 5.89 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.4
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / % possible all: 87.3

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZSJ

3zsj


Resolution: 0.9→20 Å / Num. parameters: 13462 / Num. restraintsaints: 17111 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1501 4695 5 %RANDOM
all0.1323 88644 --
obs0.1326 -95.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 29 / Occupancy sum hydrogen: 996.62 / Occupancy sum non hydrogen: 1363.35
Refinement stepCycle: LAST / Resolution: 0.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 12 262 1383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.035
X-RAY DIFFRACTIONs_zero_chiral_vol0.103
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.036
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.085

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