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- PDB-6fk2: Galectin-3 carbohydrate recognition domain in complex with lactitol -

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Basic information

Entry
Database: PDB / ID: 6fk2
TitleGalectin-3 carbohydrate recognition domain in complex with lactitol
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding domain
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsDoran, S.M.C. / Faba Rodriguez, R. / Hemmings, A.M.
CitationJournal: To be published
Title: Ligand specificity at the D-site of human Galectin-3 Carbohydrate Recognition Domain
Authors: Doran, S.M.C. / Faba Rodriguez, R. / Hemmings, A.M.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,0452
Polymers15,7011
Non-polymers3441
Water2,810156
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint4 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.295, 57.631, 62.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Fragment: carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17931
#2: Polysaccharide beta-D-galactopyranose-(1-4)-sorbitol


Type: oligosaccharide / Mass: 344.313 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[h2122h][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C6O5>]{[(1+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.14 Å3/Da / Density % sol: 42.59 % / Mosaicity: 0.06 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 4K, 0.1M MgCl2, 5mM DTT, 0.4M NaSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.84 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.01→62.6 Å / Num. obs: 71546 / % possible obs: 99.4 % / Redundancy: 6 % / Biso Wilson estimate: 10.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Net I/σ(I): 19.7 / Num. measured all: 429463
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.01-1.064.20.45999960.8870.2490.52596.6
3.19-62.65.70.03724780.9980.0160.0499.4

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AYA

3aya


Resolution: 1.01→32.04 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.04
RfactorNum. reflection% reflection
Rfree0.1409 3646 5.1 %
Rwork0.1335 --
obs0.1338 71447 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.52 Å2 / Biso mean: 15.9824 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: final / Resolution: 1.01→32.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 47 156 1311
Biso mean--25.16 27.57 -
Num. residues----138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0075-1.02080.27021260.2562417254393
1.0208-1.03470.23071160.22462489260595
1.0347-1.04950.19021480.20372534268299
1.0495-1.06520.20461270.17452562268998
1.0652-1.08180.16721500.130725832733100
1.0818-1.09960.13041280.11425832711100
1.0996-1.11850.12191590.105125912750100
1.1185-1.13890.10921340.104325872721100
1.1389-1.16080.12141550.098126122767100
1.1608-1.18450.10841340.101225752709100
1.1845-1.21020.12711460.101126262772100
1.2102-1.23840.11381560.100925812737100
1.2384-1.26940.10851390.10225932732100
1.2694-1.30370.10161540.100226042758100
1.3037-1.3420.11421430.106726002743100
1.342-1.38540.12731270.113426512778100
1.3854-1.43490.12031390.109626332772100
1.4349-1.49230.11761250.107526472772100
1.4923-1.56020.13151560.111625902746100
1.5602-1.64250.14171340.11926362770100
1.6425-1.74540.11161400.119726252765100
1.7454-1.88010.13691410.127126452786100
1.8801-2.06930.13621430.120326652808100
2.0693-2.36870.13551380.136926562794100
2.3687-2.98390.17881330.1522707284099
2.9839-32.05660.15051550.15762809296499

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