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- PDB-7cxd: Xray structure of rat Galectin-3 CRD in complex with TD-139 belon... -

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Basic information

Entry
Database: PDB / ID: 7cxd
TitleXray structure of rat Galectin-3 CRD in complex with TD-139 belonging to P121 space group
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Beta-galactose binding protein / CARBOHYDRATE / TD-139
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 / response to quercetin / 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 / regulation of T cell apoptotic process / cornified envelope / mononuclear cell migration ...negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / response to quercetin / 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 / regulation of T cell apoptotic process / cornified envelope / mononuclear cell migration / positive regulation of mononuclear cell migration / Fc-gamma receptor I complex binding / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / monosaccharide binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / Neutrophil degranulation / negative regulation of T cell receptor signaling pathway / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / immunological synapse / glial cell projection / laminin binding / neutrophil chemotaxis / extracellular matrix organization / epithelial cell differentiation / extracellular matrix / RNA splicing / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / molecular condensate scaffold activity / mRNA processing / positive regulation of angiogenesis / carbohydrate binding / protein phosphatase binding / mitochondrial inner membrane / innate immune response / external side of plasma membrane / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / extracellular space / nucleus / plasma membrane / 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
BROMIDE ION / Chem-TD2 / Galectin-3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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
B: Galectin-3
D: Galectin-3
E: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,59813
Polymers65,6034
Non-polymers2,9949
Water4,792266
1
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1293
Polymers16,4011
Non-polymers7292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1293
Polymers16,4011
Non-polymers7292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2094
Polymers16,4011
Non-polymers8083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1293
Polymers16,4011
Non-polymers7292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.241, 58.712, 70.773
Angle α, β, γ (deg.)90.000, 113.850, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 16400.873 Da / Num. of mol.: 4 / Fragment: Carbohydrare Recognition Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lgals3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08699
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: 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.: 4 / Source method: obtained synthetically / Formula: C28H30F2N6O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1.95 Å3/Da / Density % sol: 36.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 24-35% PEG 4000/6000, 0.1M Tris (pH 7.5 to pH 8.5), 0.1M MgCl2, 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: 1.078 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.71→61.5 Å / Num. obs: 48235 / % possible obs: 87.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.23 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Net I/σ(I): 9.3 / Num. measured all: 172697
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.71-1.83.70.4412791375700.9110.2670.5162.594.7
5.4-61.53.50.065632217840.9940.040.07617.899.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CXA

7cxa


Resolution: 1.71→41.17 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2405 4.99 %RANDOM
Rwork0.226 ---
obs0.227 48234 87.9 %-
Displacement parametersBiso max: 97.06 Å2 / Biso mean: 31.73 Å2 / Biso min: 12.49 Å2
Baniso -1Baniso -2Baniso -3
1-10.4427 Å20 Å20.9086 Å2
2--1.9702 Å20 Å2
3----12.4128 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 1.71→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 305 267 4859
Biso mean--30.19 36.65 -
Num. residues----550
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1615SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes924HARMONIC5
X-RAY DIFFRACTIONt_it4747HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion601SEMIHARMONIC5
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_contact5276SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4747HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6577HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion15.79
LS refinement shellResolution: 1.71→1.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.28 54 5.6 %
Rwork0.2623 911 -
all0.2633 965 -
obs--94.01 %

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