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- PDB-6l68: X-ray structure of human galectin-10 in complex with D-allose -

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Basic information

Entry
Database: PDB / ID: 6l68
TitleX-ray structure of human galectin-10 in complex with D-allose
ComponentsGalectin-10
KeywordsSUGAR BINDING PROTEIN / beta-sandwich structure / lectin
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 / collagen-containing extracellular matrix / cysteine-type endopeptidase activity / 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
beta-D-allopyranose / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsKamitori, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structures of human galectin-10/monosaccharide complexes demonstrate potential of monosaccharides as effectors in forming Charcot-Leyden crystals.
Authors: Itoh, A. / Nonaka, Y. / Nakakita, S.I. / Yoshida, H. / Nishi, N. / Nakamura, T. / Kamitori, S.
History
DepositionOct 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0043
Polymers16,6441
Non-polymers3602
Water1,08160
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0096
Polymers33,2882
Non-polymers7214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)48.900, 48.900, 259.680
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-327-

HOH

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Components

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


Mass: 16644.016 Da / Num. of mol.: 1
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: Sugar ChemComp-ALL / beta-D-allopyranose / beta-D-allose / D-allose / allose / D-ALLOPYRANOSE


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DAllpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-allopyranoseCOMMON NAMEGMML 1.0
b-D-AllpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AllSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→19.61 Å / Num. obs: 14791 / % possible obs: 97.7 % / Redundancy: 19.9 % / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 1.92→1.97 Å / Num. unique obs: 1033 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QKQ

1qkq


Resolution: 1.92→19.607 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.643 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2093 747 5.05 %
Rwork0.1804 --
all0.182 --
obs-14791 97.714 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.015 Å20.007 Å20 Å2
2--0.015 Å20 Å2
3----0.048 Å2
Refinement stepCycle: LAST / Resolution: 1.92→19.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 24 60 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131182
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171068
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.6731602
X-RAY DIFFRACTIONr_angle_other_deg1.2141.5942491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3195138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64322.90362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49515202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.763156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021278
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02248
X-RAY DIFFRACTIONr_nbd_refined0.1790.15157
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.15931
X-RAY DIFFRACTIONr_nbtor_refined0.1590.15541
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.15539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.1548
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0720.153
X-RAY DIFFRACTIONr_nbd_other0.1730.1521
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.1516
X-RAY DIFFRACTIONr_mcbond_it1.2281.717555
X-RAY DIFFRACTIONr_mcbond_other1.221.713554
X-RAY DIFFRACTIONr_mcangle_it1.9242.557692
X-RAY DIFFRACTIONr_mcangle_other1.9232.561693
X-RAY DIFFRACTIONr_scbond_it2.0982.016627
X-RAY DIFFRACTIONr_scbond_other2.0982.016627
X-RAY DIFFRACTIONr_scangle_it3.422.911910
X-RAY DIFFRACTIONr_scangle_other3.4182.913911
X-RAY DIFFRACTIONr_lrange_it4.59219.3951193
X-RAY DIFFRACTIONr_lrange_other4.59919.3341189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.92-1.9690.219390.2149940.21410790.9210.92495.73680.164
1.969-2.0230.288580.2079510.21110480.8960.92996.27860.165
2.023-2.0810.198550.1928990.1929930.940.9496.07250.15
2.081-2.1440.227510.1829060.1849890.9340.9596.76440.146
2.144-2.2140.212510.1828970.1849780.9510.95296.93250.145
2.214-2.290.195400.178630.1719300.9580.95797.09680.137
2.29-2.3750.217450.1698220.1728890.9510.9697.52530.143
2.375-2.4710.234480.1728190.1758870.9440.96297.74520.145
2.471-2.5790.206370.1758000.1768520.9610.9698.23940.147
2.579-2.7020.205430.1857550.1868120.9560.9698.27590.155
2.702-2.8460.161330.1787270.1777720.9690.96798.44560.151
2.846-3.0140.209430.1866830.1877350.9530.95898.77550.16
3.014-3.2170.223310.1876610.1896980.9540.95899.14040.169
3.217-3.4670.255290.1696320.1736650.9390.96699.39850.157
3.467-3.7860.16420.175700.1696130.9730.96799.83690.16
3.786-4.2130.176220.1665420.1665650.9710.96999.8230.16
4.213-4.8280.18270.1434870.1455160.9730.97699.61240.145
4.828-5.8260.247200.1924210.1944410.9550.9641000.187
5.826-7.8970.288200.233590.2333790.9260.9461000.207
7.897-19.6070.219130.2272550.2272680.9540.9651000.236

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