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- PDB-8yqb: Galectin-10 N32A -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8yqb
TitleGalectin-10 N32A
ComponentsGalectin-10
KeywordsSUGAR BINDING PROTEIN / Galectin-10 N32A
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: 1.95 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 N32A
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

Downloads & links

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Assembly

Deposited unit
A: Galectin-10


Theoretical massNumber of molelcules
Total (without water)16,4291
Polymers16,4291
Non-polymers00
Water3,099172
1
A: Galectin-10

A: Galectin-10


Theoretical massNumber of molelcules
Total (without water)32,8582
Polymers32,8582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)48.981, 48.981, 263.283
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-279-

HOH

21A-292-

HOH

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Components

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


Mass: 16428.809 Da / Num. of mol.: 1 / Mutation: N32A
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.: 172 / 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: 1.95→19.67 Å / Num. obs: 14787 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 13.2
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 987

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.67 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1468 10 %
Rwork0.1915 --
obs0.1942 14681 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 0 172 1293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091163
X-RAY DIFFRACTIONf_angle_d1.1791575
X-RAY DIFFRACTIONf_dihedral_angle_d21.696152
X-RAY DIFFRACTIONf_chiral_restr0.072172
X-RAY DIFFRACTIONf_plane_restr0.006202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.27531420.21481276X-RAY DIFFRACTION100
2.02-2.10.24421400.19181263X-RAY DIFFRACTION100
2.1-2.20.22281420.20091281X-RAY DIFFRACTION100
2.2-2.310.22311440.19211297X-RAY DIFFRACTION100
2.31-2.460.22681460.19411300X-RAY DIFFRACTION100
2.46-2.650.25131420.20551285X-RAY DIFFRACTION100
2.65-2.910.22391450.19431320X-RAY DIFFRACTION100
2.91-3.330.2361490.18911333X-RAY DIFFRACTION100
3.33-4.190.19711520.18291370X-RAY DIFFRACTION100
4.19-19.670.18911660.18561488X-RAY DIFFRACTION100

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