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- PDB-6b94: Crystal structure of Human galectin-1 in complex with Lactulose -

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Basic information

Entry
Database: PDB / ID: 6b94
TitleCrystal structure of Human galectin-1 in complex with Lactulose
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / Galectin-1
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
lactulose / ACETATE ION / BETA-MERCAPTOETHANOL / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsKishor, C. / Blanchard, H.
CitationJournal: Chem.Biol.Drug Des. / Year: 2018
Title: Lactulose as a novel template for anticancer drug development targeting galectins.
Authors: Kishor, C. / Ross, R.L. / Blanchard, H.
History
DepositionOct 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._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 / _entity.formula_weight
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

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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)30,80216
Polymers29,1992
Non-polymers1,60314
Water2,072115
1
A: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3327
Polymers14,5991
Non-polymers7336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4709
Polymers14,5991
Non-polymers8708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.230, 58.320, 111.500
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 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 14599.477 Da / Num. of mol.: 2
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: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-fructofuranose / lactulose


Type: oligosaccharide, Oligosaccharide / Class: Water retention / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactulose
DescriptorTypeProgram
DGalpb1-4DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 25% w/v PEG4000, 0.1 M sodium acetate trihydrate, pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 13, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→34.73 Å / Num. obs: 26735 / % possible obs: 99.7 % / Redundancy: 13.8 % / Net I/σ(I): 20.9
Reflection shellHighest resolution: 1.8 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 1.8→34.73 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.043 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23343 1365 5.1 %RANDOM
Rwork0.20917 ---
obs0.21042 25370 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→34.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 94 115 2259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022267
X-RAY DIFFRACTIONr_bond_other_d0.0030.022155
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9873057
X-RAY DIFFRACTIONr_angle_other_deg0.9933.0134953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.825288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18724.722108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2461513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02529
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3511.8361096
X-RAY DIFFRACTIONr_mcbond_other1.3491.8331094
X-RAY DIFFRACTIONr_mcangle_it2.3712.7351372
X-RAY DIFFRACTIONr_mcangle_other2.3712.7371373
X-RAY DIFFRACTIONr_scbond_it1.8022.061171
X-RAY DIFFRACTIONr_scbond_other1.8022.061171
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5133.0131676
X-RAY DIFFRACTIONr_long_range_B_refined4.63814.92299
X-RAY DIFFRACTIONr_long_range_B_other4.59914.7782268
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 100 -
Rwork0.245 1789 -
obs--98.8 %

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