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- PDB-7cxb: Structure of mouse Galectin-3 CRD in complex with TD-139 belongin... -

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Basic information

Entry
Database: PDB / ID: 7cxb
TitleStructure of mouse Galectin-3 CRD in complex with TD-139 belonging to P6522 space group.
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / beta-galactose binding protein / CARBOHYDRATE
Function / homology
Function and homology information


negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / 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 / cornified envelope / negative regulation of endocytosis / IgE binding / Fc-gamma receptor I complex binding ...negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / 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 / cornified envelope / negative regulation of endocytosis / IgE binding / Fc-gamma receptor I complex binding / eosinophil chemotaxis / monosaccharide binding / negative regulation of T cell receptor signaling pathway / positive chemotaxis / positive regulation of calcium ion import / macrophage chemotaxis / monocyte chemotaxis / glial cell projection / immunological synapse / laminin binding / Neutrophil degranulation / RNA splicing / extracellular matrix organization / neutrophil chemotaxis / extracellular matrix / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / spliceosomal complex / mRNA processing / positive regulation of angiogenesis / collagen-containing extracellular matrix / cell differentiation / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / nucleus / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-TD2 / Galectin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsKumar, A.
CitationJournal: Glycobiology / Year: 2021
Title: Molecular mechanism of interspecies differences in the binding affinity of TD139 to Galectin-3.
Authors: Kumar, A. / Paul, M. / Panda, M. / Jayaram, S. / Kalidindi, N. / Sale, H. / Vetrichelvan, M. / Gupta, A. / Mathur, A. / Beno, B. / Regueiro-Ren, A. / Cheng, D. / Ramarao, M. / Ghosh, K.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)19,3233
Polymers18,6391
Non-polymers6842
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.880, 63.880, 136.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21A-486-

HOH

31A-532-

HOH

41A-540-

HOH

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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 / IgE-binding protein / L-34 galactoside-binding lectin / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 18639.246 Da / Num. of mol.: 1 / Fragment: Carbohydrate Recognition Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lgals3 / Production host: Escherichia coli (E. coli) / References: UniProt: P16110
#2: Chemical ChemComp-TD2 / 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside


Mass: 648.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30F2N6O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 24%-35% (PEG 4000/PEG 6000), 0.1M Tris (pH 7.5 to pH 8.5), 0.4M NaSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.46→55.32 Å / Num. obs: 29378 / % possible obs: 99.8 % / Redundancy: 20.1 % / Biso Wilson estimate: 22.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.02 / Rrim(I) all: 0.087 / Net I/σ(I): 19.3 / Num. measured all: 591876 / Scaling rejects: 1
Reflection shellResolution: 1.46→1.5 Å / Redundancy: 21.2 % / Rmerge(I) obs: 1.599 / Num. measured all: 44742 / Num. unique obs: 2113 / CC1/2: 0.834 / Rpim(I) all: 0.353 / Rrim(I) all: 1.638 / Net I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CXA

7cxa


Resolution: 1.46→51.26 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1425 4.86 %RANDOM
Rwork0.194 ---
obs0.196 29306 99.8 %-
Displacement parametersBiso max: 75.49 Å2 / Biso mean: 24.36 Å2 / Biso min: 12.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.0245 Å20 Å20 Å2
2---2.0245 Å20 Å2
3---4.049 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.46→51.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 151 163 1408
Biso mean--18.21 36.12 -
Num. residues----138
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d538SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes462HARMONIC5
X-RAY DIFFRACTIONt_it2417HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion169SEMIHARMONIC5
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_contact2558SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2417HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4365HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion4.44
X-RAY DIFFRACTIONt_other_torsion14.86
LS refinement shellResolution: 1.46→1.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2309 40 6.81 %
Rwork0.2331 547 -
all0.233 587 -
obs--99.65 %

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