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- PDB-8yqa: Galectin-10 L27A -

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Basic information

Entry
Database: PDB / ID: 8yqa
TitleGalectin-10 L27A
ComponentsGalectin-10
KeywordsSUGAR BINDING PROTEIN / Galectin-10 L27A
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: 2.17 Å
AuthorsSu, J.Y. / Sun, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171255 China
CitationJournal: To Be Published
Title: Galectin-10 L27A
Authors: Su, J.Y. / Sun, Y.Q.
History
DepositionMar 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-10


Theoretical massNumber of molelcules
Total (without water)16,4301
Polymers16,4301
Non-polymers00
Water1,31573
1
A: Galectin-10

A: Galectin-10


Theoretical massNumber of molelcules
Total (without water)32,8602
Polymers32,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area1680 Å2
ΔGint-3 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.679, 48.679, 259.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

21A-251-

HOH

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Components

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


Mass: 16429.752 Da / Num. of mol.: 1 / Mutation: L27A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.17→19.98 Å / Num. obs: 10513 / % possible obs: 98.7 % / Redundancy: 30.7 % / Rmerge(I) obs: 0.187 / Net I/σ(I): 16.3
Reflection shellResolution: 2.17→2.24 Å / Rmerge(I) obs: 0.705 / Num. unique obs: 895

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→19.53 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 1042 10.01 %
Rwork0.2057 --
obs0.2101 10413 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 0 73 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091143
X-RAY DIFFRACTIONf_angle_d1.0811550
X-RAY DIFFRACTIONf_dihedral_angle_d6.931149
X-RAY DIFFRACTIONf_chiral_restr0.064169
X-RAY DIFFRACTIONf_plane_restr0.005200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.280.20831440.19781300X-RAY DIFFRACTION100
2.28-2.430.26491470.20851314X-RAY DIFFRACTION100
2.43-2.610.29211440.22161298X-RAY DIFFRACTION100
2.61-2.880.29161490.22851342X-RAY DIFFRACTION100
2.88-3.290.27861490.22971338X-RAY DIFFRACTION100
3.29-4.140.23361410.19371274X-RAY DIFFRACTION92
4.14-19.530.22251680.19091505X-RAY DIFFRACTION100

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