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- PDB-8jae: Crystal structure of E33A mutant human galectin-10 produced by ce... -

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Basic information

Entry
Database: PDB / ID: 8jae
TitleCrystal structure of E33A mutant human galectin-10 produced by cell-free protein synthesis in complex with melezitose
ComponentsGalectin-10
KeywordsSUGAR BINDING PROTEIN / Galectin / CLC
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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsKojima, M. / Ueno, T. / Abe, S. / Hirata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Cell-free protein crystallization for rapid structure determination of multiple substrates
Authors: Kojima, M. / Abe, S. / Hirata, K. / Ueno, T.
History
DepositionMay 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9182
Polymers16,4141
Non-polymers5041
Water2,810156
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8364
Polymers32,8282
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area4010 Å2
ΔGint18 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.160, 49.160, 262.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-280-

HOH

21A-312-

HOH

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Components

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


Mass: 16413.797 Da / Num. of mol.: 1 / Mutation: E33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free synthesis / Gene: CLC, LGALS10, LGALS10A / Production host: Triticum aestivum (bread wheat) / References: UniProt: Q05315
#2: Polysaccharide alpha-D-glucopyranose-(1-2)-[alpha-D-glucopyranose-(1-3)]beta-D-fructofuranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-2[DGlcpa1-3]DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-1/a1-b2_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}[(3+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: small tubes / Details: cell-free crystallization

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 25346 / % possible obs: 99.8 % / Redundancy: 14.47 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.988 / Net I/σ(I): 10.52
Reflection shellResolution: 1.62→1.72 Å / Num. unique obs: 4028 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Coot0.8.9.2 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→42.57 Å / SU ML: 0.196 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2217 1997 7.91 %
Rwork0.194 23244 -
obs0.1962 25241 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.7 Å2
Refinement stepCycle: LAST / Resolution: 1.62→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 34 156 1328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711247
X-RAY DIFFRACTIONf_angle_d1.01091703
X-RAY DIFFRACTIONf_chiral_restr0.0674194
X-RAY DIFFRACTIONf_plane_restr0.0067211
X-RAY DIFFRACTIONf_dihedral_angle_d6.666168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.29491370.32991602X-RAY DIFFRACTION99.66
1.66-1.710.3151400.27541625X-RAY DIFFRACTION99.94
1.71-1.760.2771400.23591629X-RAY DIFFRACTION100
1.76-1.810.24441380.21841599X-RAY DIFFRACTION100
1.81-1.880.24551370.20431606X-RAY DIFFRACTION100
1.88-1.950.22561390.21561626X-RAY DIFFRACTION100
1.95-2.040.26331410.22521639X-RAY DIFFRACTION100
2.04-2.150.22021400.17911629X-RAY DIFFRACTION100
2.15-2.280.20621410.19061638X-RAY DIFFRACTION100
2.28-2.460.19941430.18291679X-RAY DIFFRACTION100
2.46-2.710.22311430.1861661X-RAY DIFFRACTION100
2.71-3.10.20681470.19261696X-RAY DIFFRACTION99.95
3.1-3.90.19071480.1771726X-RAY DIFFRACTION100
3.91-42.570.22091630.16811889X-RAY DIFFRACTION99.61

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