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- PDB-5nfc: Structure of Galectin-3 CRD in complex with glycerol -

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Basic information

Entry
Database: PDB / ID: 5nfc
TitleStructure of Galectin-3 CRD in complex with glycerol
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Galectin-3 CRD / cation-Pi interactions
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / 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 / macrophage chemotaxis / positive chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / molecular condensate scaffold activity / neutrophil chemotaxis / secretory granule membrane / RNA splicing / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein-containing complex assembly / positive regulation of protein localization to plasma membrane / spliceosomal complex / 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 / membrane / nucleus / 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: 1.59 Å
AuthorsRonin, C. / Atmanene, C. / Gautier, F.M. / Djedaini Pilard, F. / Teletchea, S. / Ciesielski, F. / Vivat Hannah, V. / Grandjean, C.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Biophysical and structural characterization of mono/di-arylated lactosamine derivatives interaction with human galectin-3.
Authors: Atmanene, C. / Ronin, C. / Teletchea, S. / Gautier, F.M. / Djedaini-Pilard, F. / Ciesielski, F. / Vivat, V. / Grandjean, C.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Derived calculations
Category: pdbx_data_processing_status / struct_conn / struct_conn_type
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,5512
Polymers16,4591
Non-polymers921
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.750, 58.290, 62.870
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: 16458.844 Da / Num. of mol.: 1 / Fragment: UNP residues 106-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.05 Å3/Da / Density % sol: 27.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris HCl pH7.5; 30-34% PEG4000; 100mM MgCl2; 400mM NaSCN; 8mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 18644 / % possible obs: 98.8 % / Redundancy: 6.1 % / Rsym value: 0.036 / Net I/σ(I): 33.9
Reflection shellResolution: 1.59→1.68 Å / Rsym value: 0.073

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zsl

3zsl


Resolution: 1.59→42.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.231 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18386 933 5 %RANDOM
Rwork0.14593 ---
obs0.14786 17711 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.602 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.59→42.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 6 142 1256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191241
X-RAY DIFFRACTIONr_bond_other_d0.0010.021228
X-RAY DIFFRACTIONr_angle_refined_deg2.2191.9541702
X-RAY DIFFRACTIONr_angle_other_deg0.97532828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97723.8163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59915219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6551511
X-RAY DIFFRACTIONr_chiral_restr0.150.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211440
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02309
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3691.184587
X-RAY DIFFRACTIONr_mcbond_other1.3421.181586
X-RAY DIFFRACTIONr_mcangle_it2.0491.777741
X-RAY DIFFRACTIONr_mcangle_other2.0551.779742
X-RAY DIFFRACTIONr_scbond_it2.6181.476654
X-RAY DIFFRACTIONr_scbond_other2.6181.476654
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8732.115951
X-RAY DIFFRACTIONr_long_range_B_refined5.58610.7861350
X-RAY DIFFRACTIONr_long_range_B_other5.34910.1451290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.587→1.628 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 66 -
Rwork0.136 1238 -
obs--96.59 %

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