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

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Basic information

Entry
Database: PDB / ID: 9uwu
TitleCrystal structure of human galectin-10 produced by cell-free protein synthesis in complex with melezitose
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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

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Assembly

Deposited unit
A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0383
Polymers16,4721
Non-polymers5672
Water1,47782
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0776
Polymers32,9442
Non-polymers1,1334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area1950 Å2
ΔGint-0 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.470, 49.470, 263.790
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-339-

HOH

21A-355-

HOH

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Components

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


Mass: 16471.832 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-glucopyranose-(1-2)-[alpha-D-glucopyranose-(1-3)]beta-D-fructofuranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-2[DGlcpa1-3]DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-1/a1-b2_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}[(3+1)][a-D-Glcp]{}}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.: 82 / 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: Feb 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 14256 / % possible obs: 99.9 % / Redundancy: 15.7 % / Biso Wilson estimate: 21.12 Å2 / CC1/2: 0.985 / Net I/σ(I): 6.5
Reflection shellResolution: 1.99→2.11 Å / Num. unique obs: 2179 / CC1/2: 0.669 / % 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: 1.99→43.96 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.3096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 1415 10 %
Rwork0.2011 12735 -
obs0.2059 14150 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.44 Å2
Refinement stepCycle: LAST / Resolution: 1.99→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 38 82 1248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871222
X-RAY DIFFRACTIONf_angle_d1.13451664
X-RAY DIFFRACTIONf_chiral_restr0.068188
X-RAY DIFFRACTIONf_plane_restr0.0091206
X-RAY DIFFRACTIONf_dihedral_angle_d8.0361159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.060.32041370.25631238X-RAY DIFFRACTION100
2.06-2.140.29141360.23441222X-RAY DIFFRACTION100
2.14-2.240.26291370.23131228X-RAY DIFFRACTION100
2.24-2.360.25591370.21731236X-RAY DIFFRACTION100
2.36-2.510.28161380.21191249X-RAY DIFFRACTION100
2.51-2.70.25471400.2111253X-RAY DIFFRACTION100
2.7-2.970.28681410.20211264X-RAY DIFFRACTION100
2.97-3.40.2381420.20491282X-RAY DIFFRACTION100
3.4-4.280.20091470.17291324X-RAY DIFFRACTION99.86
4.29-43.960.2341600.18081439X-RAY DIFFRACTION99.19

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