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- PDB-9uwo: Crystal structure of human galectin-10 produced by cell-free prot... -

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Basic information

Entry
Database: PDB / ID: 9uwo
TitleCrystal structure of human galectin-10 produced by cell-free protein synthesis in complex with sucrose
ComponentsGalectin-10
KeywordsSUGAR BINDING PROTEIN / Galectin / CLC
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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
sucrose / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsKojima, M. / Ueno, T. / Abe, S. / Hirata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Small Struct / Year: 2025
Title: Cell-Free Protein Crystallization Enables Rapid Structure Determination of Disaccharides and Trisaccharides Using Galectin-10 Crystals.
Authors: Kojima, M. / Yao, X. / Abe, S. / Furuta, T. / Hirata, K. / Kobayashi, R. / Suzuki, T. / Ueno, T.
History
DepositionMay 12, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8422
Polymers16,5001
Non-polymers3421
Water2,486138
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6844
Polymers33,0002
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area1660 Å2
ΔGint-2 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.250, 49.250, 262.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-278-

HOH

21A-295-

HOH

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Components

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


Mass: 16499.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Production host: Triticum aestivum (bread wheat) / References: UniProt: Q05315
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 55.68 %
Crystal growTemperature: 293 K / Method: small tubes / Details: cell-free crystallization

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 24512 / % possible obs: 99.9 % / Redundancy: 70.1 % / Biso Wilson estimate: 14.44 Å2 / CC1/2: 0.991 / Net I/σ(I): 23.1
Reflection shellResolution: 1.64→1.74 Å / Num. unique obs: 3819 / CC1/2: 0.639 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→42.65 Å / SU ML: 0.1988 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.085
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 1998 8.21 %
Rwork0.211 22337 -
obs0.2135 24335 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.01 Å2
Refinement stepCycle: LAST / Resolution: 1.64→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 0 23 138 1283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781220
X-RAY DIFFRACTIONf_angle_d1.11691667
X-RAY DIFFRACTIONf_chiral_restr0.0731185
X-RAY DIFFRACTIONf_plane_restr0.0075210
X-RAY DIFFRACTIONf_dihedral_angle_d8.4939177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.38371330.36921480X-RAY DIFFRACTION97.58
1.68-1.730.35151380.30251524X-RAY DIFFRACTION98.99
1.73-1.780.32261400.27441579X-RAY DIFFRACTION99.77
1.78-1.830.30151380.241545X-RAY DIFFRACTION99.76
1.83-1.90.30571410.24321570X-RAY DIFFRACTION99.88
1.9-1.980.27971390.25261558X-RAY DIFFRACTION99.88
1.98-2.070.22231410.21831574X-RAY DIFFRACTION100
2.07-2.180.22361390.19951567X-RAY DIFFRACTION99.88
2.18-2.310.22391430.19051589X-RAY DIFFRACTION100
2.31-2.490.21961430.19481606X-RAY DIFFRACTION100
2.49-2.740.24151450.19481621X-RAY DIFFRACTION99.89
2.74-3.140.22341460.2031624X-RAY DIFFRACTION100
3.14-3.950.2191480.18641670X-RAY DIFFRACTION100
3.95-42.650.21151640.19021830X-RAY DIFFRACTION99.8

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