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- PDB-3oyw: Crystal structure of human galectin-1 in complex with thiodigalac... -

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Basic information

Entry
Database: PDB / ID: 3oyw
TitleCrystal structure of human galectin-1 in complex with thiodigalactoside
Components(Galectin-1) x 2
KeywordsCARBOHYDRATE BINDING PROTEIN / Galectin / Lactobionic acid
Function / homology
Function and homology information


galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / receptor ligand activity / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / extracellular exosome / extracellular region / 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
thiodigalactoside / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsBlanchard, H. / Collins, P.M.
CitationJournal: CANCER LETT. / Year: 2010
Title: Galectin inhibitory disaccharides promote tumour immunity in a breast cancer model
Authors: Stannard, K.A. / Collins, P.M. / Ito, K. / Sullivan, E.M. / Scott, S.A. / Gabutero, E. / Darren Grice, I. / Low, P. / Nilsson, U.J. / Leffler, H. / Blanchard, H. / Ralph, S.J.
History
DepositionSep 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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 / 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 / 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_atom_id / _atom_site.label_comp_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.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 12, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_branch_scheme / pdbx_molecule_features / struct_conn
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 / _chem_comp.pdbx_synonyms / _pdbx_branch_scheme.pdb_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id
Revision 3.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1924
Polymers29,4752
Non-polymers7172
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.368, 58.367, 111.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-1 / Gal-1 / Lectin galactoside-binding soluble 1 / Beta-galactoside-binding lectin L-14-I / Lactose- ...Gal-1 / Lectin galactoside-binding soluble 1 / Beta-galactoside-binding lectin L-14-I / Lactose-binding lectin 1 / S-Lac lectin 1 / Galaptin / 14 kDa lectin / HPL / HBL / Putative MAPK-activating protein PM12 / 14 kDa laminin-binding protein / HLBP14


Mass: 14707.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Protein Galectin-1 / Gal-1 / Lectin galactoside-binding soluble 1 / Beta-galactoside-binding lectin L-14-I / Lactose- ...Gal-1 / Lectin galactoside-binding soluble 1 / Beta-galactoside-binding lectin L-14-I / Lactose-binding lectin 1 / S-Lac lectin 1 / Galaptin / 14 kDa lectin / HPL / HBL / Putative MAPK-activating protein PM12 / 14 kDa laminin-binding protein / HLBP14


Mass: 14767.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#3: Polysaccharide beta-D-galactopyranose-(1-1)-1-thio-beta-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 358.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides, and with reducing-end-to-reducing-end glycosidic bond
References: thiodigalactoside
DescriptorTypeProgram
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Galp1SH]{[(1+S)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 4-8 microlitre drops consisting of equal volumes of protein solution (20 mM sodium potassium phosphate buffer, pH 7.0, and protein at concentration of 10 mg/mL) and reservoir solution (0.2 M ...Details: 4-8 microlitre drops consisting of equal volumes of protein solution (20 mM sodium potassium phosphate buffer, pH 7.0, and protein at concentration of 10 mg/mL) and reservoir solution (0.2 M ammonium sulphate, 25% w/v polyethylene glycol 4000, 0.1M sodium acetate trihydrate, pH 6.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 9, 2008
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→55.9 Å / Num. all: 10154 / Num. obs: 10154 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.6 Å / % possible all: 80.8

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
REFMAC5.2.0019refinement
SAINTdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→55.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.532 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.698 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24492 480 4.7 %RANDOM
Rwork0.16701 ---
obs0.17068 9645 95.2 %-
all-10154 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.616 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2---2.6 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 46 66 2176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9812964
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.1815.216278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86525.14107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26615329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6921511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211679
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2781
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21436
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.68521346
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.14732152
X-RAY DIFFRACTIONr_scbond_it4.6714839
X-RAY DIFFRACTIONr_scangle_it7.3586811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.495→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 26 -
Rwork0.207 598 -
obs--80.52 %

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