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- PDB-6y78: Structure of galectin-3C in complex with lactose determined by se... -

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Basic information

Entry
Database: PDB / ID: 6y78
TitleStructure of galectin-3C in complex with lactose determined by serial crystallography using a silicon nitride membrane support
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / galectin / synchrotron serial crystallography / solid support / silicon nitride membranel
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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-lactose / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHakansson, M. / Welin, M. / Shilova, A. / Kovacic, R. / Mueller, U. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Vinnova2018-04409 Sweden
CitationJournal: J.Synchrotron Radiat. / Year: 2020
Title: Current status and future opportunities for serial crystallography at MAX IV Laboratory.
Authors: Shilova, A. / Lebrette, H. / Aurelius, O. / Nan, J. / Welin, M. / Kovacic, R. / Ghosh, S. / Safari, C. / Friel, R.J. / Milas, M. / Matej, Z. / Hogbom, M. / Branden, G. / Kloos, M. / Shoeman, ...Authors: Shilova, A. / Lebrette, H. / Aurelius, O. / Nan, J. / Welin, M. / Kovacic, R. / Ghosh, S. / Safari, C. / Friel, R.J. / Milas, M. / Matej, Z. / Hogbom, M. / Branden, G. / Kloos, M. / Shoeman, R.L. / Doak, B. / Ursby, T. / Hakansson, M. / Logan, D.T. / Mueller, U.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)16,0432
Polymers15,7011
Non-polymers3421
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint2 kcal/mol
Surface area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.670, 56.360, 61.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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
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.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 32303

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were grown on XtalTool supports (Jena Bioscience) over a 24 well VDX-plate with 1 ml reservoir. The drop was made up of 1 microlitre 20 mg/ml protein in 10 mM sodium phosphate pH 7. ...Details: Crystals were grown on XtalTool supports (Jena Bioscience) over a 24 well VDX-plate with 1 ml reservoir. The drop was made up of 1 microlitre 20 mg/ml protein in 10 mM sodium phosphate pH 7.4, 100 mM NaCl, 10 mM beta-mercaptoethanol, 2 mM lactose, 0.25 microlitres of galectin-3C seed crystals in a stabilization solution containing 0.1 M Tris pH 7.5, 33% (w/v) PEG 4000, 0.1 M MgCl2, 0.2 M NaSCN and 0.75 microlitres reservoir solution containing 0.1 M Tris pH 7.5, 34% (w/v) PEG 4000, 0.2 M NaSCN and 8 mM beta-mercapthoethanol. Crystals grew to a size of approximately 10-15 micrometer.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2019
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→61 Å / Num. obs: 14154 / % possible obs: 100 % / Redundancy: 195.2 % / Biso Wilson estimate: 21.27 Å2 / R split: 0.155 / Net I/σ(I): 5.3
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 133.1 % / Mean I/σ(I) obs: 1.41 / Num. unique obs: 1369 / R split: 1.833 / % possible all: 100
Serial crystallography measurementSource size: 100 µm2
Serial crystallography sample deliveryDescription: silicon nitride membrane (Silson) / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: silicon nitride membrane / Motion control: MD3 (Arinax) / Sample dehydration prevention: membrane sandwich / Support base: cryo cap
Serial crystallography data reductionFrame hits: 21029 / Frames failed index: 7507 / Frames indexed: 13522 / Frames total: 32303

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EYM

6eym


Resolution: 1.7→41.45 Å / SU ML: 0.1801 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.9329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 678 4.99 %
Rwork0.1656 12908 -
obs0.1672 13586 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.49 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 23 73 1202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01991214
X-RAY DIFFRACTIONf_angle_d1.59331665
X-RAY DIFFRACTIONf_chiral_restr0.0636191
X-RAY DIFFRACTIONf_plane_restr0.0085219
X-RAY DIFFRACTIONf_dihedral_angle_d13.0291475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.29651170.25122257X-RAY DIFFRACTION86.33
1.83-2.020.23251300.17462548X-RAY DIFFRACTION96.23
2.02-2.310.20311350.15622609X-RAY DIFFRACTION98.81
2.31-2.910.1851500.17462678X-RAY DIFFRACTION99.72
2.91-41.450.18371460.15322816X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 12.6737030943 Å / Origin y: 0.42243450904 Å / Origin z: 6.2913268179 Å
111213212223313233
T0.126981289561 Å20.00384425539812 Å2-0.0227704047979 Å2-0.144844972328 Å2-0.00306944044697 Å2--0.120903534827 Å2
L1.30698630371 °20.453715315946 °2-0.662799809079 °2-2.59295220083 °2-1.34351359642 °2--2.88373755161 °2
S0.0252464820698 Å °-0.00968382959128 Å °-0.116037686713 Å °-0.0338675423209 Å °-0.0373211789152 Å °-0.0425147890315 Å °0.200967969458 Å °0.0724438077038 Å °0.00548596782862 Å °
Refinement TLS groupSelection details: all

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