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- PDB-7xxu: Macaca fascicularis galectin-10/Charcot-Leyden crystal protein -

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Basic information

Entry
Database: PDB / ID: 7xxu
TitleMacaca fascicularis galectin-10/Charcot-Leyden crystal protein
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / Macaca fascicularis galectin-10/Charcot-Leyden crystal protein
Function / homology
Function and homology information


carbohydrate binding
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 speciesMacaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSu, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2023
Title: Glutathione disrupts galectin-10 Charcot-Leyden crystal formation to possibly ameliorate eosinophil-based diseases such as asthma.
Authors: Na, H. / Sayed, H. / Ayala, G.J. / Wang, X. / Liu, Y. / Yu, J. / Liu, T. / Mayo, K.H. / Su, J.
History
DepositionMay 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin


Theoretical massNumber of molelcules
Total (without water)16,1981
Polymers16,1981
Non-polymers00
Water3,297183
1
A: Galectin

A: Galectin


Theoretical massNumber of molelcules
Total (without water)32,3972
Polymers32,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area1640 Å2
ΔGint-5 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.530, 48.530, 258.914
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-226-

HOH

21A-247-

HOH

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Components

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


Mass: 16198.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: EGM_09723 / Production host: Escherichia coli (E. coli) / References: UniProt: G7PXK5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
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: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→19.99 Å / Num. obs: 17996 / % possible obs: 99.9 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 20.1
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.379 / Num. unique obs: 1029

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XRG

5xrg


Resolution: 1.8→19.99 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 18.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1789 10 %
Rwork0.1843 16093 -
obs0.1876 17882 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.22 Å2 / Biso mean: 20.3367 Å2 / Biso min: 6.85 Å2
Refinement stepCycle: final / Resolution: 1.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 0 183 1302
Biso mean---30.17 -
Num. residues----136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.850.24871310.213911861317
1.85-1.90.28181330.211411931326
1.9-1.960.27481330.21211971330
1.96-2.030.23181370.193812291366
2.03-2.120.22811330.185511961329
2.12-2.210.23161370.198312301367
2.21-2.330.22711330.183811941327
2.33-2.470.23781350.198112241359
2.47-2.660.24791360.196312251361
2.66-2.930.2291380.184212411379
2.93-3.350.16441410.181812661407
3.35-4.220.20341440.163112961440
4.22-19.990.19711580.173214161574

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