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- PDB-5xrm: Galectin-10/Charcot-Leyden crystal protein variant W72A crystal s... -

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Basic information

Entry
Database: PDB / ID: 5xrm
TitleGalectin-10/Charcot-Leyden crystal protein variant W72A crystal structure
ComponentsGalectin-10
KeywordsPROTEIN BINDING / Galectin-10/Charcot-Leyden crystal protein
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. / 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 / Resolution: 1.998 Å
AuthorsSu, J.
CitationJournal: Glycobiology / Year: 2018
Title: Galectin-10: a new structural type of prototype galectin dimer and effects on saccharide ligand binding.
Authors: Su, J. / Gao, J. / Si, Y. / Cui, L. / Song, C. / Wang, Y. / Wu, R. / Tai, G. / Zhou, Y.
History
DepositionJun 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7312
Polymers16,6391
Non-polymers921
Water2,486138
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4624
Polymers33,2782
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2170 Å2
ΔGint-6 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.830, 48.830, 260.335
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-349-

HOH

21A-392-

HOH

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Components

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


Mass: 16638.977 Da / Num. of mol.: 1 / Mutation: W72A
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.998→19.59 Å / Num. obs: 13511 / % possible obs: 99.3 % / Redundancy: 17.9 % / Net I/σ(I): 34.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
RefinementResolution: 1.998→19.59 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.41 / Phase error: 17.86
RfactorNum. reflection% reflection
Rfree0.2078 1342 10 %
Rwork0.1696 --
obs0.1734 13414 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.95 Å2 / Biso mean: 18.3131 Å2 / Biso min: 7.35 Å2
Refinement stepCycle: final / Resolution: 1.998→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 6 138 1260
Biso mean--36.12 27.74 -
Num. residues----141

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