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- PDB-6a1v: Charcot-Leyden crystal protein/Galectin-10 variant E33Q -

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Basic information

Entry
Database: PDB / ID: 6a1v
TitleCharcot-Leyden crystal protein/Galectin-10 variant E33Q
ComponentsGalectin-10
KeywordsPROTEIN BINDING / Charcot-Leyden crystal protein/Galectin-10 variant E33Q
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 / cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate binding / collagen-containing extracellular matrix / 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.984 Å
AuthorsSu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500637 China
CitationJournal: Glycobiology / Year: 2019
Title: Identification of key amino acid residues determining ligand binding specificity, homodimerization and cellular distribution of human galectin-10
Authors: Su, J. / Song, C. / Si, Y. / Cui, L. / Yang, T. / Li, Y. / Wang, H. / Tai, G. / Zhou, Y.
History
DepositionJun 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,7531
Polymers16,7531
Non-polymers00
Water2,612145
1
A: Galectin-10

A: Galectin-10


Theoretical massNumber of molelcules
Total (without water)33,5062
Polymers33,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area1730 Å2
ΔGint-4 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.967, 48.967, 259.759
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-273-

HOH

21A-290-

HOH

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Components

#1: Protein Galectin-10 / Gal-10 / Charcot-Leyden crystal protein


Mass: 16753.123 Da / Num. of mol.: 1 / Fragment: UNP residues 2-142 / Mutation: E33Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC / Production host: Escherichia coli (E. coli) / References: UniProt: Q05315
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Bistris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.98→19.98 Å / Num. obs: 13899 / % possible obs: 99.9 % / Redundancy: 3.4 % / Net I/σ(I): 8.8
Reflection shellResolution: 1.98→2.03 Å

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Processing

SoftwareName: PHENIX / Version: (1.13_2998: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.984→19.631 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.12
RfactorNum. reflection% reflection
Rfree0.232 1340 10 %
Rwork0.1986 --
obs0.2018 13404 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.61 Å2 / Biso mean: 24.2757 Å2 / Biso min: 12.64 Å2
Refinement stepCycle: final / Resolution: 1.984→19.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 0 145 1275
Biso mean---33.1 -
Num. residues----141

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