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- PDB-7cxc: Structure of mouse Galectin-3 CRD point mutant (V160A) in complex... -

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Basic information

Entry
Database: PDB / ID: 7cxc
TitleStructure of mouse Galectin-3 CRD point mutant (V160A) 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 immunological synapse formation / 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 / negative regulation of T cell receptor signaling pathway / immunological synapse / glial cell projection / Neutrophil degranulation / extracellular matrix organization ...negative regulation of immunological synapse formation / 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 / negative regulation of T cell receptor signaling pathway / immunological synapse / glial cell projection / Neutrophil degranulation / extracellular matrix organization / extracellular matrix / RNA splicing / skeletal system development / spliceosomal complex / mRNA processing / : / carbohydrate binding / cell differentiation / innate immune response / external side of plasma membrane / 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: 1.4 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5204
Polymers37,2222
Non-polymers1,2972
Water4,648258
1
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2602
Polymers18,6111
Non-polymers6491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2602
Polymers18,6111
Non-polymers6491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.513, 58.286, 68.085
Angle α, β, γ (deg.)90.000, 103.560, 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 / L-34 galactoside-binding lectin / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 18611.191 Da / Num. of mol.: 2 / Fragment: Carbohydrate Recognition Domain / Mutation: V160A
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.: 2 / Source method: obtained synthetically / Formula: C28H30F2N6O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.84 Å3/Da / Density % sol: 33.16 %
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), 0.4M 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: 1.12713 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.4→58.29 Å / Num. obs: 53247 / % possible obs: 77.7 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 16.9 / Num. measured all: 244146
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
1.14-1.220.159501524990.9530.1510.22417.6
3.6-58.293.20.045928328890.9840.0320.05528.790.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CXB

7cxb


Resolution: 1.4→43.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.527 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 2566 5 %RANDOM
Rwork0.1442 ---
obs0.1459 48248 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.31 Å2 / Biso mean: 14.564 Å2 / Biso min: 3.97 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å2-0 Å22.2 Å2
2--2.78 Å20 Å2
3---1.07 Å2
Refinement stepCycle: final / Resolution: 1.4→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 300 258 2684
Biso mean--9.44 24.4 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172269
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.7563312
X-RAY DIFFRACTIONr_angle_other_deg0.761.6435124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9425284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30221.933119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05315356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0941516
X-RAY DIFFRACTIONr_chiral_restr0.1270.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
X-RAY DIFFRACTIONr_rigid_bond_restr4.29734687
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 160 -
Rwork0.122 3604 -
all-3764 -
obs--95.36 %

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