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- PDB-6rzi: Galectin-3C in complex with trifluoroaryltriazole monothiogalacto... -

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Basic information

Entry
Database: PDB / ID: 6rzi
TitleGalectin-3C in complex with trifluoroaryltriazole monothiogalactoside derivative:1(Hydrogen)
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 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 / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding ...: / 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 / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / 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 / macrophage chemotaxis / 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 / neutrophil chemotaxis / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / 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 / 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-KP8 / THIOCYANATE ION / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.095 Å
AuthorsKumar, R. / Verteramo, M.L. / Nilsson, U.J. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2013.0022 Sweden
CitationJournal: to be published
Title: Thermodynamic studies of halogen-bond interactions in galectin-3
Authors: Verteramo, M.L. / Zetterberg, F. / Kumar, R. / Wallerstein, J. / Ignjatovic, M.M. / Leffler, H. / Ryde, U. / Logan, D.T. / Akke, M. / Nilsson, U.J.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)16,2133
Polymers15,7011
Non-polymers5122
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-3 kcal/mol
Surface area7220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.152, 56.822, 61.591
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
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-KP8 / (2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-phenylsulfanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol


Mass: 453.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18F3N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 0.1 M Tris/HCl pH 7.5, 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 IV / Beamline: BioMAX / Wavelength: 0.652 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.652 Å / Relative weight: 1
ReflectionResolution: 1.095→28.41 Å / Num. obs: 52849 / % possible obs: 99.8 % / Redundancy: 13.3 % / Net I/σ(I): 11.62
Reflection shellResolution: 1.095→1.135 Å / Num. unique obs: 5170

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZSL

3zsl


Resolution: 1.095→28.411 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 2632 4.99 %
Rwork0.1544 --
obs0.1558 52776 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.095→28.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 34 214 1354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151194
X-RAY DIFFRACTIONf_angle_d1.4131628
X-RAY DIFFRACTIONf_dihedral_angle_d16.83450
X-RAY DIFFRACTIONf_chiral_restr0.111181
X-RAY DIFFRACTIONf_plane_restr0.01213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0955-1.11540.35631290.33972512X-RAY DIFFRACTION97
1.1154-1.13690.3481310.30042602X-RAY DIFFRACTION100
1.1369-1.16010.34231330.27522625X-RAY DIFFRACTION100
1.1601-1.18530.27751570.25852588X-RAY DIFFRACTION100
1.1853-1.21290.29231390.24442606X-RAY DIFFRACTION100
1.2129-1.24320.27861420.22372605X-RAY DIFFRACTION100
1.2432-1.27680.28051180.20682625X-RAY DIFFRACTION100
1.2768-1.31440.24251380.19172613X-RAY DIFFRACTION100
1.3144-1.35680.2151110.18472649X-RAY DIFFRACTION100
1.3568-1.40530.22091200.17312652X-RAY DIFFRACTION100
1.4053-1.46160.19751300.14742640X-RAY DIFFRACTION100
1.4616-1.52810.1911490.12832621X-RAY DIFFRACTION100
1.5281-1.60860.17641570.11172620X-RAY DIFFRACTION100
1.6086-1.70940.14711560.10872635X-RAY DIFFRACTION100
1.7094-1.84140.14051400.11132637X-RAY DIFFRACTION100
1.8414-2.02660.13991490.11032668X-RAY DIFFRACTION100
2.0266-2.31980.14621330.12212693X-RAY DIFFRACTION100
2.3198-2.92220.16851470.16282712X-RAY DIFFRACTION100
2.9222-28.42050.18841530.16152841X-RAY DIFFRACTION100

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