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- PDB-5yt4: Galectin-10 variant H53A soaked in glycerol for 5 minutes -

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Basic information

Entry
Database: PDB / ID: 5yt4
TitleGalectin-10 variant H53A soaked in glycerol for 5 minutes
ComponentsGalectin-10
KeywordsCELL ADHESION / Galectin-10
Function / homology
Function and homology information


regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / : / carbohydrate binding / identical protein binding / cytosol
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSu, J.
CitationJournal: Glycobiology / Year: 2018
Title: Galectin-10: a new structural type of prototype galectin dimer and effects on saccharide ligand binding.
Authors: Su, J. / Gao, J. / Si, Y. / Cui, L. / Song, C. / Wang, Y. / Wu, R. / Tai, G. / Zhou, Y.
History
DepositionNov 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9662
Polymers15,8741
Non-polymers921
Water2,162120
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9324
Polymers31,7482
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2300 Å2
ΔGint-3 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.741, 48.741, 257.663
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21A-363-

HOH

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Components

#1: Protein Galectin-10 / Gal-10 / Charcot-Leyden crystal protein / CLC / Eosinophil lysophospholipase / Lysolecithin acylhydrolase


Mass: 15874.033 Da / Num. of mol.: 1 / Mutation: H53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Production host: Escherichia coli (E. coli) / References: UniProt: Q05315
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2→19.531 Å / Num. obs: 13190 / % possible obs: 99.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.307 / Num. unique obs: 949 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.22data extraction
RefinementResolution: 2→19.531 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.7
RfactorNum. reflection% reflection
Rfree0.2167 1316 10.01 %
Rwork0.1824 --
obs0.1858 13148 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.95 Å2 / Biso mean: 21.3534 Å2 / Biso min: 10.83 Å2
Refinement stepCycle: final / Resolution: 2→19.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 6 120 1208
Biso mean--35.59 31.53 -
Num. residues----138

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