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- PDB-6l6d: X-ray structure of human galectin-10 in complex with D-N-acetylga... -

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Basic information

Entry
Database: PDB / ID: 6l6d
TitleX-ray structure of human galectin-10 in complex with D-N-acetylgalactosamine
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 / 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
2-acetamido-2-deoxy-beta-D-galactopyranose / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 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)16,8652
Polymers16,6441
Non-polymers2211
Water1,26170
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7304
Polymers33,2882
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area1670 Å2
ΔGint-6 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.900, 48.900, 261.660
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-356-

HOH

21A-357-

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-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
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: Aug 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→19.63 Å / Num. obs: 14992 / % possible obs: 99.8 % / Redundancy: 19.3 % / CC1/2: 0.998 / Net I/σ(I): 16.8
Reflection shellResolution: 1.93→1.98 Å / Num. unique obs: 1048 / CC1/2: 0.903

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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: 1.93→19.628 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.315 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2332 759 5.063 %
Rwork0.2017 --
all0.203 --
obs-14992 99.814 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.848 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20.001 Å20 Å2
2--0.001 Å20 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.93→19.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 15 70 1244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131202
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171099
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.6651626
X-RAY DIFFRACTIONr_angle_other_deg1.1891.5882558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0765141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52222.564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40715212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.931157
X-RAY DIFFRACTIONr_chiral_restr0.0570.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02258
X-RAY DIFFRACTIONr_nbd_refined0.170.15160
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.15975
X-RAY DIFFRACTIONr_nbtor_refined0.1590.15552
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.15585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.1570
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0830.1512
X-RAY DIFFRACTIONr_nbd_other0.1540.1535
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.1517
X-RAY DIFFRACTIONr_mcbond_it1.0681.74567
X-RAY DIFFRACTIONr_mcbond_other1.0681.736566
X-RAY DIFFRACTIONr_mcangle_it1.782.592707
X-RAY DIFFRACTIONr_mcangle_other1.7792.597708
X-RAY DIFFRACTIONr_scbond_it1.6351.979635
X-RAY DIFFRACTIONr_scbond_other1.6341.979636
X-RAY DIFFRACTIONr_scangle_it2.6532.873919
X-RAY DIFFRACTIONr_scangle_other2.6512.873920
X-RAY DIFFRACTIONr_lrange_it3.91519.4291242
X-RAY DIFFRACTIONr_lrange_other3.91519.361237
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
1.93-1.980.244500.229980.22110480.9010.9131000.19
1.98-2.0330.271500.21410040.21710540.8890.9171000.185
2.033-2.0920.314570.2149320.229890.8970.921000.183
2.092-2.1550.241570.1999320.2019890.9120.9351000.173
2.155-2.2250.236470.1999310.2019780.9360.9381000.172
2.225-2.3020.281520.2048470.2088990.9010.9311000.174
2.302-2.3880.321480.2048500.2098980.8650.9341000.175
2.388-2.4840.241440.2068300.2088740.9220.9371000.181
2.484-2.5920.233470.227910.228380.9360.9361000.195
2.592-2.7160.288350.2087800.2118150.9110.9431000.181
2.716-2.860.261290.1987330.2017620.930.9481000.177
2.86-3.030.288390.2176990.227380.8980.9371000.196
3.03-3.2340.223330.2036570.2046900.940.951000.187
3.234-3.4850.223340.2066270.2076610.9470.9521000.197
3.485-3.8050.218340.1985700.1996040.960.9591000.189
3.805-4.2350.158290.1715360.175650.9770.971000.171
4.235-4.8520.145250.1594850.1585100.9880.9741000.165
4.852-5.8540.22190.2044210.2054400.9680.9651000.202
5.854-7.9330.31190.2183560.2213750.9220.9591000.216
7.933-19.6280.17110.2382540.2352660.9810.96499.62410.254

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