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- PDB-6l64: X-ray structure of human galectin-10 in complex with D-glucose -

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Basic information

Entry
Database: PDB / ID: 6l64
TitleX-ray structure of human galectin-10 in complex with D-glucose
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 / 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-glucopyranose / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 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)17,1844
Polymers16,6441
Non-polymers5403
Water54030
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3698
Polymers33,2882
Non-polymers1,0816
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)48.650, 48.650, 259.230
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-308-

HOH

21A-319-

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-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


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


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
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 MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→19.52 Å / Num. obs: 11869 / % possible obs: 99.8 % / Redundancy: 19.4 % / CC1/2: 0.998 / Net I/σ(I): 15.1
Reflection shellResolution: 2.08→2.13 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 832 / 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: 2.08→19.517 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.326 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2357 564 4.752 %
Rwork0.1987 --
all0.2 --
obs-11869 99.773 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20 Å20 Å2
2--0.001 Å20 Å2
3----0.003 Å2
Refinement stepCycle: LAST / Resolution: 2.08→19.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 36 30 1190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131188
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171072
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6871611
X-RAY DIFFRACTIONr_angle_other_deg1.1591.6062502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3955137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.89722.90362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11615201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.076156
X-RAY DIFFRACTIONr_chiral_restr0.0580.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021271
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02247
X-RAY DIFFRACTIONr_nbd_refined0.1850.15152
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.15971
X-RAY DIFFRACTIONr_nbtor_refined0.1620.15524
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.15580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.1541
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.159
X-RAY DIFFRACTIONr_nbd_other0.1840.1534
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.158
X-RAY DIFFRACTIONr_mcbond_it1.2632.158551
X-RAY DIFFRACTIONr_mcbond_other1.2632.152550
X-RAY DIFFRACTIONr_mcangle_it1.9653.222687
X-RAY DIFFRACTIONr_mcangle_other1.9643.229688
X-RAY DIFFRACTIONr_scbond_it2.1052.571637
X-RAY DIFFRACTIONr_scbond_other2.1042.57637
X-RAY DIFFRACTIONr_scangle_it3.3213.75924
X-RAY DIFFRACTIONr_scangle_other3.323.756925
X-RAY DIFFRACTIONr_lrange_it4.74224.1321166
X-RAY DIFFRACTIONr_lrange_other4.56824.1111165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.08-2.1330.225410.2387910.2378320.9150.9050.204
2.133-2.1910.303400.2247790.2278190.8940.9220.189
2.191-2.2540.203420.2157580.2158000.9230.9290.183
2.254-2.3220.298420.2097350.2147770.910.9280.176
2.322-2.3970.26380.2157100.2177480.8950.9210.181
2.397-2.480.262360.2277030.2297390.9180.9210.187
2.48-2.5720.248370.2086730.217100.9120.9280.175
2.572-2.6750.223330.2136430.2146760.9210.930.183
2.675-2.7920.272260.2096360.2126620.9180.9350.176
2.792-2.9250.296350.2145980.2196330.9180.930.177
2.925-3.0790.215320.2065830.2066150.9210.9450.173
3.079-3.2610.201290.1965570.1965860.9590.9550.162
3.261-3.4790.15190.1785400.1775590.9610.9610.155
3.479-3.7480.246210.1794820.1815030.9420.9620.161
3.748-4.0910.207190.1724690.1744880.9750.9710.156
4.091-4.5490.138220.1484160.1484380.9840.9810.136
4.549-5.2060.267120.1523970.1554090.9640.9810.146
5.206-6.2650.261180.2243440.2263620.9560.9570.198
6.265-8.4360.38690.2422930.2453020.9130.9440.211
8.436-19.5170.262130.2521980.2532110.9620.9580.232

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