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- PDB-7xxz: Macaca mulatta galectin-10/Charcot-Leyden crystal protein with gl... -

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Basic information

Entry
Database: PDB / ID: 7xxz
TitleMacaca mulatta galectin-10/Charcot-Leyden crystal protein with glycerol
ComponentsGalectin-10/Charcot-Leyden crystal protein
KeywordsSUGAR BINDING PROTEIN / Macaca mulatta galectin-10/Charcot-Leyden crystal protein with glycerol
Function / homologyJelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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)16,5932
Polymers16,5011
Non-polymers921
Water3,675204
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)33,1864
Polymers33,0012
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2100 Å2
ΔGint-6 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.720, 48.720, 259.204
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-307-

HOH

21A-347-

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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
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: 1.83→19.54 Å / Num. obs: 17232 / % possible obs: 99.6 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 0.65 / Num. unique obs: 1034

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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: 1.83→19.54 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 1711 10 %
Rwork0.177 15402 -
obs0.1801 17113 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.76 Å2 / Biso mean: 20.9469 Å2 / Biso min: 11.25 Å2
Refinement stepCycle: final / Resolution: 1.83→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 6 204 1342
Biso mean--30.38 31.03 -
Num. residues----138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.880.26441380.234212391377100
1.88-1.940.26691360.20111236137299
1.94-2.010.21061380.18491241137999
2.01-2.090.26091370.165312371374100
2.09-2.190.18851410.175212641405100
2.19-2.310.23351400.17912631403100
2.31-2.450.19861410.17461264140599
2.45-2.640.23271400.18812631403100
2.64-2.90.19341430.187212921435100
2.9-3.320.18981450.182113071452100
3.32-4.180.20791500.157913461496100
4.18-19.540.18571620.17151450161299

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