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- PDB-9il3: Crystal structure of human malectin in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 9il3
TitleCrystal structure of human malectin in complex with glucose
ComponentsMalectin
KeywordsSUGAR BINDING PROTEIN / Qulity / ER / N-glycosylation
Function / homology
Function and homology information


oligosaccharyltransferase complex / specific granule membrane / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / carbohydrate binding / endoplasmic reticulum membrane / Neutrophil degranulation / enzyme binding / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Malectin / Malectin domain / Malectin domain
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / alpha-D-glucopyranose / Malectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSi, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82201916 China
CitationJournal: To Be Published
Title: The Structural Basis of Human Malectin Recognition of Ligands
Authors: Si, Y.L.
History
DepositionJun 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malectin
B: Malectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2328
Polymers41,5032
Non-polymers7296
Water8,377465
1
A: Malectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1164
Polymers20,7521
Non-polymers3643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area9540 Å2
MethodPISA
2
B: Malectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1164
Polymers20,7521
Non-polymers3643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-14 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.510, 100.510, 36.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Malectin


Mass: 20751.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLEC, KIAA0152 / Production host: Escherichia (bacteria) / References: UniProt: Q14165
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES pH7.5, 2.0M Ammonium sulphate, 10% 1,4-Dioxane, 20mM Glucose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 76210 / % possible obs: 100 % / Redundancy: 9.64 % / CC1/2: 0.964 / Net I/σ(I): 25.01
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 6626 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPXdata processing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→33.27 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 2019 2.8 %
Rwork0.1775 --
obs0.1781 72104 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 10 465 3439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123040
X-RAY DIFFRACTIONf_angle_d1.1264118
X-RAY DIFFRACTIONf_dihedral_angle_d6.174402
X-RAY DIFFRACTIONf_chiral_restr0.096448
X-RAY DIFFRACTIONf_plane_restr0.01532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.27441420.20184987X-RAY DIFFRACTION100
1.49-1.530.20791440.19295083X-RAY DIFFRACTION100
1.53-1.570.20531440.18214998X-RAY DIFFRACTION100
1.57-1.620.20941380.18984992X-RAY DIFFRACTION100
1.62-1.680.2651500.19024972X-RAY DIFFRACTION100
1.68-1.750.22241420.18294998X-RAY DIFFRACTION100
1.75-1.830.20531460.18555011X-RAY DIFFRACTION100
1.83-1.920.20691460.19344994X-RAY DIFFRACTION100
1.92-2.040.22031460.18575022X-RAY DIFFRACTION100
2.04-2.20.18641440.17774987X-RAY DIFFRACTION100
2.2-2.420.19491440.18335028X-RAY DIFFRACTION100
2.42-2.770.21491440.19575006X-RAY DIFFRACTION100
2.77-3.490.22141480.17654996X-RAY DIFFRACTION100
3.49-33.270.13971410.14575011X-RAY DIFFRACTION100

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