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- PDB-9uwn: Crystal structure of E33A mutant of human galectin-10 produced by... -

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Basic information

Entry
Database: PDB / ID: 9uwn
TitleCrystal structure of E33A mutant of human galectin-10 produced by cell-free protein synthesis in complex with raffinose
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
raffinose / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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)16,9803
Polymers16,4141
Non-polymers5672
Water3,297183
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9616
Polymers32,8282
Non-polymers1,1334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area3960 Å2
ΔGint17 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.190, 49.190, 261.800
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-358-

HOH

21A-416-

HOH

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Components

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


Mass: 16413.797 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 alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 27731 / % possible obs: 100 % / Redundancy: 23.9 % / Biso Wilson estimate: 15.08 Å2 / CC1/2: 1 / Net I/σ(I): 43.5
Reflection shellResolution: 1.57→1.63 Å / Num. unique obs: 4553 / CC1/2: 0.995 / % possible all: 100

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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: 1.57→40.51 Å / SU ML: 0.1667 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2097 2000 7.25 %
Rwork0.1851 25594 -
obs0.1869 27594 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.5 Å2
Refinement stepCycle: LAST / Resolution: 1.57→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 38 183 1348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711229
X-RAY DIFFRACTIONf_angle_d1.54941671
X-RAY DIFFRACTIONf_chiral_restr0.2612187
X-RAY DIFFRACTIONf_plane_restr0.0081209
X-RAY DIFFRACTIONf_dihedral_angle_d7.0677160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.25331380.22141769X-RAY DIFFRACTION99.9
1.61-1.650.23581390.20881775X-RAY DIFFRACTION100
1.65-1.70.24031400.19471791X-RAY DIFFRACTION100
1.7-1.760.25241390.18551780X-RAY DIFFRACTION100
1.76-1.820.19751390.18411778X-RAY DIFFRACTION100
1.82-1.890.20831420.18641812X-RAY DIFFRACTION100
1.89-1.980.20921380.18631769X-RAY DIFFRACTION100
1.98-2.080.20591400.18961793X-RAY DIFFRACTION100
2.08-2.210.20961420.18031812X-RAY DIFFRACTION100
2.21-2.380.18441410.18151821X-RAY DIFFRACTION100
2.38-2.620.22071440.18631838X-RAY DIFFRACTION100
2.62-30.2131460.18361866X-RAY DIFFRACTION99.95
3-3.780.20081490.18291917X-RAY DIFFRACTION100
3.78-40.510.20591630.182073X-RAY DIFFRACTION99.87

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