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- PDB-6eol: Human galectin-3c in complex with a galactose derivative -

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Basic information

Entry
Database: PDB / ID: 6eol
TitleHuman galectin-3c in complex with a galactose derivative
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN
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 / epithelial cell differentiation / molecular condensate scaffold activity / neutrophil chemotaxis / RNA splicing / secretory granule membrane / positive regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / 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-BKH / THIOCYANATE ION / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsHakansson, M. / Nilsson, U.J. / Zetterberg, F. / Logan, D.T.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council621-2012-2978 Sweden
Knut and Alice Wallenberg Foundation2013.0022 Sweden
CitationJournal: ChemMedChem / Year: 2018
Title: Monosaccharide Derivatives with Low-Nanomolar Lectin Affinity and High Selectivity Based on Combined Fluorine-Amide, Phenyl-Arginine, Sulfur-pi , and Halogen Bond Interactions.
Authors: Zetterberg, F.R. / Peterson, K. / Johnsson, R.E. / Brimert, T. / Hakansson, M. / Logan, D.T. / Leffler, H. / Nilsson, U.J.
History
DepositionOct 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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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)16,3744
Polymers15,7351
Non-polymers6383
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint0 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.152, 58.260, 62.797
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
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-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-BKH / (2~{R},3~{R},4~{S},5~{R},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol


Mass: 522.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16Cl2F3N3O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 20 MG/ML GALECTIN-3C, 100MM NACL, 30 % W/V PEG 4000, 0.4 M NASCN, 8 MM BETA-MERCAPTOETHANOL, 10 MM PHOSHATE, 100 MM MGCL2, 100 MM TRIS/HCL PH 7.5, 1.0 MM LIGAND

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 2014
RadiationMonochromator: BENT SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 21720 / % possible obs: 99.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementResolution: 1.5→29.13 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.09 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1110 5.11 %RANDOM
Rwork0.17 ---
obs0.172 21720 99.3 %-
Displacement parametersBiso mean: 19.13 Å2
Baniso -1Baniso -2Baniso -3
1--5.7713 Å20 Å20 Å2
2--4.196 Å20 Å2
3---1.5753 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.5→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 39 212 1360
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012747HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185019HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d627SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes445HARMONIC5
X-RAY DIFFRACTIONt_it2747HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.84
X-RAY DIFFRACTIONt_other_torsion14.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion179SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3225SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.57 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2754 148 5.36 %
Rwork0.2142 2611 -
all0.2172 2759 -
obs--96.16 %
Refinement TLS params.Method: refined / Origin x: -12.7842 Å / Origin y: -0.7496 Å / Origin z: 6.3555 Å
111213212223313233
T0.0036 Å20.0027 Å20.0048 Å2--0.0293 Å2-0.0051 Å2---0.0583 Å2
L0.1606 °20.1085 °20.1017 °2-1.0675 °20.8129 °2--1.4507 °2
S0.0005 Å °0.0014 Å °0.0233 Å °0.0042 Å °-0.0025 Å °0.0157 Å °-0.0514 Å °-0.0293 Å °0.002 Å °
Refinement TLS groupSelection details: { A|* }

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