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- PDB-7xxy: Macaca mulatta galectin-10/Charcot-Leyden crystal protein with lactose -

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Basic information

Entry
Database: PDB / ID: 7xxy
TitleMacaca mulatta galectin-10/Charcot-Leyden crystal protein with lactose
ComponentsGalectin-10/Charcot-Leyden crystal protein
KeywordsSUGAR BINDING PROTEIN / Macaca mulatta galectin-10/Charcot-Leyden crystal protein with lactose
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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-10/Charcot-Leyden crystal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8432
Polymers16,5011
Non-polymers3421
Water2,342130
1
A: Galectin-10/Charcot-Leyden crystal protein
hetero molecules

A: Galectin-10/Charcot-Leyden crystal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6864
Polymers33,0012
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3060 Å2
ΔGint4 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.609, 48.609, 256.265
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-283-

HOH

21A-300-

HOH

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Components

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


Mass: 16500.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.56 %
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: Jan 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.92→19.47 Å / Num. obs: 14830 / % possible obs: 99.9 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 21.1
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.741 / Num. unique obs: 941

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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: 1.92→19.47 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1472 10 %
Rwork0.1739 13243 -
obs0.1774 14715 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.92 Å2 / Biso mean: 25.4857 Å2 / Biso min: 15.87 Å2
Refinement stepCycle: final / Resolution: 1.92→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1126 0 23 130 1279
Biso mean--33.92 33.98 -
Num. residues----137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.92-1.980.22421260.173111411267
1.98-2.050.20251320.162611711303
2.05-2.130.22171270.156411531280
2.13-2.230.17371320.161511841316
2.23-2.350.19191300.162711681298
2.35-2.50.23031320.162311821314
2.5-2.690.19931340.178311991333
2.69-2.960.22261320.186311921324
2.96-3.380.25491360.192312301366
3.38-4.260.19551390.163812541393
4.26-19.470.19881520.180613691521

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