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- PDB-4y24: Complex of human Galectin-1 and TD-139 -

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Basic information

Entry
Database: PDB / ID: 4y24
TitleComplex of human Galectin-1 and TD-139
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / Complex / Galectin-1 / TDG / TD-139
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
Chem-TD2 / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å
AuthorsLin, H.Y. / Hsieh, T.J. / Lin, C.H.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Academia SinicaAS-022316 Taiwan
Ministry of Science and Technology103-2113-M-001-023-MY3 Taiwan
Ministry of Science and Technology102-2113-M-001-001-MY3 Taiwan
Ministry of Science and Technology102-2923-M-001-001-MY3 Taiwan
CitationJournal: Sci Rep / Year: 2016
Title: Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors.
Authors: Hsieh, T.J. / Lin, H.Y. / Tu, Z. / Lin, T.C. / Wu, S.C. / Tseng, Y.Y. / Liu, F.T. / Hsu, S.T. / Lin, C.H.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)34,9594
Polymers33,6622
Non-polymers1,2972
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.578, 58.242, 110.976
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-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: 16830.965 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) / Strain (production host): BL21(DE3) / References: UniProt: P09382
#2: Chemical ChemComp-TD2 / 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside


Mass: 648.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30F2N6O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris (pH 8.0), 0.2 M Li2SO4, 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. obs: 12357 / % possible obs: 96.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 19.79 Å2 / Rmerge(I) obs: 0.092 / Χ2: 0.971 / Net I/av σ(I): 22.942 / Net I/σ(I): 10.8 / Num. measured all: 87647
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.32-2.45.30.27410690.94486.3
2.4-2.55.80.2711390.92490.5
2.5-2.616.30.26611840.88993.7
2.61-2.756.90.23112000.93396.2
2.75-2.927.40.19412540.91297.9
2.92-3.157.90.17312470.92299.5
3.15-3.468.20.11512750.93999.9
3.46-3.968.10.07212860.895100
3.96-4.997.60.06113041.27899.9
4.99-3070.04913991.01599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→29.538 Å / FOM work R set: 0.8191 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1103 9.96 %
Rwork0.2004 9970 -
obs0.2053 11073 86.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.87 Å2 / Biso mean: 32.26 Å2 / Biso min: 9.9 Å2
Refinement stepCycle: final / Resolution: 2.32→29.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 90 96 2224
Biso mean--51.65 35.41 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042182
X-RAY DIFFRACTIONf_angle_d0.772966
X-RAY DIFFRACTIONf_chiral_restr0.024304
X-RAY DIFFRACTIONf_plane_restr0.004390
X-RAY DIFFRACTIONf_dihedral_angle_d27.806880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.42560.3177960.227686395961
2.4256-2.55340.291120.24721004111671
2.5534-2.71320.28671250.23421132125781
2.7132-2.92260.28211400.22841248138887
2.9226-3.21640.28171430.22791312145593
3.2164-3.6810.24261550.19041418157399
3.681-4.63480.20121620.159114591621100
4.6348-29.540.22281700.19271534170499

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