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- PDB-6h64: Crystal structure of the CRD-SAT -

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Basic information

Entry
Database: PDB / ID: 6h64
TitleCrystal structure of the CRD-SAT
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / carbohydrate recognition domain
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / 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 / macrophage chemotaxis / regulation of T cell proliferation / 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 / molecular condensate scaffold activity / neutrophil chemotaxis / RNA splicing / secretory granule membrane / positive regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / mRNA processing / carbohydrate binding / collagen-containing extracellular matrix / protein phosphatase binding / 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
alpha-lactose / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCharron, C. / Kriznik, A. / Yelehe-Okouma, M. / Jouzeau, J.-Y. / Reboul, P.
CitationJournal: Biotechnol J / Year: 2019
Title: CRD SAT Generated by pCARGHO: A New Efficient Lectin-Based Affinity Tag Method for Safe, Simple, and Low-Cost Protein Purification.
Authors: Kriznik, A. / Yelehe-Okouma, M. / Lec, J.C. / Groshenry, G. / Le Cordier, H. / Charron, C. / Quinternet, M. / Mazon, H. / Talfournier, F. / Boschi-Muller, S. / Jouzeau, J.Y. / Reboul, P.
History
DepositionJul 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: 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.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 16, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _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 2.2Jan 17, 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
B: Galectin-3
C: Galectin-3
D: Galectin-3
E: Galectin-3
F: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,93721
Polymers113,0196
Non-polymers2,91815
Water8,233457
1
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3714
Polymers18,8361
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3714
Polymers18,8361
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3714
Polymers18,8361
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2753
Polymers18,8361
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2753
Polymers18,8361
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2753
Polymers18,8361
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.058, 118.058, 137.506
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11B-652-

HOH

21E-651-

HOH

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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: 18836.426 Da / Num. of mol.: 6
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)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6M magnesium sulfate, 100 mM MES at pH 6.5, 2 mM lactose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 98662 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rsym value: 0.049 / Net I/σ(I): 33.3
Reflection shellResolution: 1.8→1.91 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R9B

4r9b


Resolution: 1.8→10 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.238 --
Rwork0.201 --
obs-98662 99.35 %
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 183 457 7245

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