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- PDB-4lbn: Crystal structure of Human galectin-3 CRD in complex with LNnT -

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Basic information

Entry
Database: PDB / ID: 4lbn
TitleCrystal structure of Human galectin-3 CRD in complex with LNnT
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / galectin / carbohydrate-recognition / LNnT / glycosphingolipid / beta sandwich / carbohydrate binding protein
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration / 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 / positive chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / macrophage chemotaxis / 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 / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / 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 / extracellular space / RNA binding / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCollins, P.M. / Blanchard, H.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Galectin-3 interactions with glycosphingolipids.
Authors: Collins, P.M. / Bum-Erdene, K. / Yu, X. / Blanchard, H.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: 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)16,6086
Polymers15,7581
Non-polymers8495
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.551, 57.875, 63.510
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: 15758.100 Da / Num. of mol.: 1 / Fragment: unp residues 112-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17931
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1a_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-2/a4-b1_b3-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 31% PEG 6000, 100MM MGCL2, 8MM BETA MERCEPTOETHANOL, 100MM TRIS HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54184 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.491→42.778 Å / Num. all: 14618 / Num. obs: 14618 / % possible obs: 94.8 % / Redundancy: 7.2 % / Rsym value: 0.089 / Net I/σ(I): 19.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.792.60.1554416115760.15572.3
1.79-1.93.10.1374.4582318980.13791.9
1.9-2.033.80.1164.9743819800.116100
2.03-2.194.60.1174.7839218220.117100
2.19-2.47.10.1441226617170.14100
2.4-2.6910.80.1274.41681915520.127100
2.69-3.111.60.114.91609013830.11100
3.1-3.812.90.0965.51524011770.096100
3.8-5.3813.50.0727.2127869490.072100
5.38-57.87512.30.0559.369495640.05599.8

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
PROTEUM PLUSdata collection
SAINTdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1A3K

1a3k


Resolution: 1.7→42.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1853 / WRfactor Rwork: 0.1643 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8871 / SU B: 3.522 / SU ML: 0.058 / SU R Cruickshank DPI: 0.1086 / SU Rfree: 0.0977 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 739 5.1 %RANDOM
Rwork0.1546 ---
obs0.1558 14575 94.71 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso max: 128.63 Å2 / Biso mean: 22.3708 Å2 / Biso min: 6.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0 Å2
2---0.12 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 52 116 1280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191267
X-RAY DIFFRACTIONr_bond_other_d00.021225
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9921738
X-RAY DIFFRACTIONr_angle_other_deg0.64432815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6665164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90824.35562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95415212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.825159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_mcbond_it3.1822.984584
X-RAY DIFFRACTIONr_mcbond_other3.162.976583
X-RAY DIFFRACTIONr_mcangle_it4.0844.954736
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 43 -
Rwork0.202 711 -
all-754 -
obs--67.02 %
Refinement TLS params.Method: refined / Origin x: 12.5948 Å / Origin y: 0.8743 Å / Origin z: 6.8665 Å
111213212223313233
T0.0081 Å2-0.0007 Å2-0.0074 Å2-0.0258 Å20.0138 Å2--0.0258 Å2
L0.5042 °20.1729 °2-0.2397 °2-1.0987 °2-0.6515 °2--1.6116 °2
S0.0427 Å °-0.015 Å °-0.0483 Å °0.0033 Å °-0.0016 Å °0.0413 Å °0.0534 Å °0.0443 Å °-0.0411 Å °

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