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- PDB-6fof: Crystal structure of a crystallized variant of h-Gal3: Gal-3[NTS/... -

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Basic information

Entry
Database: PDB / ID: 6fof
TitleCrystal structure of a crystallized variant of h-Gal3: Gal-3[NTS/VII-IX]
ComponentsGalectin-3,Galectin-3
KeywordsSUGAR BINDING PROTEIN / Galectin / apoptosis / glycosylation
Function / homology
Function and homology information


negative regulation of NK T cell activation / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / 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 / receptor ligand inhibitor activity / 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 / signaling receptor inhibitor activity / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / Advanced glycosylation endproduct receptor signaling / immunological synapse / ficolin-1-rich granule membrane / laminin binding / neutrophil chemotaxis / epithelial cell differentiation / RNA splicing / secretory granule membrane / 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 / : / carbohydrate binding / protein phosphatase binding / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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
beta-lactose / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRomero, A. / Flores-Ibarra, A. / Medrano, F.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBFU2016-77835-R Spain
CitationJournal: Sci Rep / Year: 2018
Title: Crystallization of a human galectin-3 variant with two ordered segments in the shortened N-terminal tail.
Authors: Flores-Ibarra, A. / Vertesy, S. / Medrano, F.J. / Gabius, H.J. / Romero, A.
History
DepositionFeb 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_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
C: Galectin-3,Galectin-3
D: Galectin-3,Galectin-3
E: Galectin-3,Galectin-3
G: Galectin-3,Galectin-3
A: Galectin-3,Galectin-3
B: Galectin-3,Galectin-3
F: Galectin-3,Galectin-3
H: Galectin-3,Galectin-3
I: Galectin-3,Galectin-3
J: Galectin-3,Galectin-3
K: Galectin-3,Galectin-3
L: Galectin-3,Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,93148
Polymers254,51812
Non-polymers6,41336
Water2,306128
1
C: Galectin-3,Galectin-3
D: Galectin-3,Galectin-3
E: Galectin-3,Galectin-3
G: Galectin-3,Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16918
Polymers84,8394
Non-polymers2,33014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Galectin-3,Galectin-3
B: Galectin-3,Galectin-3
F: Galectin-3,Galectin-3
H: Galectin-3,Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,88115
Polymers84,8394
Non-polymers2,04211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
I: Galectin-3,Galectin-3
J: Galectin-3,Galectin-3
K: Galectin-3,Galectin-3
L: Galectin-3,Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,88115
Polymers84,8394
Non-polymers2,04211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.851, 98.195, 237.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Galectin-3,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: 21209.848 Da / Num. of mol.: 12
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: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.78 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% PEG 8K, 100 mM Tris-HCl (pH 8.5), 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→49.1 Å / Num. obs: 112248 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 43.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rsym value: 0.142 / Net I/σ(I): 11.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.233 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 16179 / CC1/2: 0.558 / Rsym value: 1.308 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A3K

1a3k


Resolution: 2.2→49.1 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 5607 5 %Random
Rwork0.213 ---
obs-106537 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å2-0 Å2-0 Å2
2---0.85 Å20 Å2
3---2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13564 0 396 128 14088
LS refinement shellResolution: 2.2→2.26 Å
RfactorNum. reflection% reflection
Rfree0.35 413 5 %
Rwork0.342 7797 -
obs--99.97 %

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