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- PDB-6i74: Galectin-3C in complex with substituted polyfluoroaryl monothioga... -

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Basic information

Entry
Database: PDB / ID: 6i74
TitleGalectin-3C in complex with substituted polyfluoroaryl monothiogalactoside derivative 1
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE-BINDING PROTEIN / GALACTOSE-SPECIFIC LECTIN 3 / GALACTOSIDE-BINDING PROTEIN / GALBP / IGE-6 BINDING PROTEIN / L-31 / LAMININ-BINDING PROTEIN / LECTIN L-29 / MAC-2
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 / positive chemotaxis / macrophage 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 / spliceosomal complex / molecular condensate scaffold activity / 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 / mRNA processing / carbohydrate binding / collagen-containing extracellular matrix / protein phosphatase binding / 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
Chem-H5Z / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.959 Å
AuthorsKumar, R. / Peterson, K. / Nilsson, U.J. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2013.0022 Sweden
CitationJournal: Org. Biomol. Chem. / Year: 2019
Title: Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects.
Authors: Kumar, R. / Peterson, K. / Misini Ignjatovic, M. / Leffler, H. / Ryde, U. / Nilsson, U.J. / Logan, D.T.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2042
Polymers15,7011
Non-polymers5031
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.654, 57.781, 62.755
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: 15701.049 Da / Num. of mol.: 1 / Fragment: UNP residues 113-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17931
#2: Chemical ChemComp-H5Z / (2~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-4-[4-[2,3,4,5,6-pentakis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol


Mass: 503.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18F5N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 4000, 0.1 M Tris/HCl pH 7.5, 0.1 M MgCl2, 0.4 M NaSCN, 7.9 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2015
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.959→26.24 Å / Num. obs: 77623 / % possible obs: 94.39 % / Redundancy: 5.8 % / Biso Wilson estimate: 7.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04265 / Rpim(I) all: 0.01922 / Net I/av σ(I): 24.15 / Net I/σ(I): 24.15
Reflection shellResolution: 0.959→0.9938 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.207 / Mean I/σ(I) obs: 0.93 / CC1/2: 0.409 / Rpim(I) all: 0.7081 / % possible all: 78.51

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Processing

Software
NameVersionClassification
PHENIX(dev_3084: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ZSL
Resolution: 0.959→27.574 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 14.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1473 3898 5.03 %
Rwork0.1318 --
obs0.1326 77549 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.959→27.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 34 236 1376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111256
X-RAY DIFFRACTIONf_angle_d1.2271725
X-RAY DIFFRACTIONf_dihedral_angle_d12.774486
X-RAY DIFFRACTIONf_chiral_restr0.109189
X-RAY DIFFRACTIONf_plane_restr0.008227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9595-0.97120.4456650.4021694X-RAY DIFFRACTION61
0.9712-0.98350.40891340.35492322X-RAY DIFFRACTION85
0.9835-0.99640.27041200.26952591X-RAY DIFFRACTION92
0.9964-1.01010.23551340.21732560X-RAY DIFFRACTION93
1.0101-1.02450.22121150.19352536X-RAY DIFFRACTION93
1.0245-1.03980.181330.17042616X-RAY DIFFRACTION94
1.0398-1.05610.15211410.16382570X-RAY DIFFRACTION94
1.0561-1.07340.161570.14622571X-RAY DIFFRACTION94
1.0734-1.09190.17081320.14012611X-RAY DIFFRACTION94
1.0919-1.11170.15211500.13362565X-RAY DIFFRACTION93
1.1117-1.13310.14121410.13182633X-RAY DIFFRACTION95
1.1331-1.15620.14641430.12092564X-RAY DIFFRACTION94
1.1562-1.18140.15541210.11512671X-RAY DIFFRACTION95
1.1814-1.20890.12841290.10512654X-RAY DIFFRACTION96
1.2089-1.23910.11571360.10062649X-RAY DIFFRACTION96
1.2391-1.27260.12981400.09912679X-RAY DIFFRACTION97
1.2726-1.310.13581580.09992662X-RAY DIFFRACTION96
1.31-1.35230.1121450.10382696X-RAY DIFFRACTION97
1.3523-1.40070.12741440.10752718X-RAY DIFFRACTION98
1.4007-1.45670.1241310.10282733X-RAY DIFFRACTION98
1.4567-1.5230.12271490.10422729X-RAY DIFFRACTION98
1.523-1.60330.12441380.10542761X-RAY DIFFRACTION98
1.6033-1.70380.1271760.11192724X-RAY DIFFRACTION99
1.7038-1.83530.13981620.11812758X-RAY DIFFRACTION99
1.8353-2.01990.1161700.11452806X-RAY DIFFRACTION99
2.0199-2.31210.12141300.11912828X-RAY DIFFRACTION99
2.3121-2.91250.15811330.14362879X-RAY DIFFRACTION100
2.9125-27.58550.16491710.14962871X-RAY DIFFRACTION96

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