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- PDB-9ikp: Crystal structure of human malectin -

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Basic information

Entry
Database: PDB / ID: 9ikp
TitleCrystal structure of human malectin
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 / Malectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 28, 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)41,8716
Polymers41,5032
Non-polymers3684
Water8,827490
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.656, 100.656, 36.188
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: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES pH7.0, 2.0M ammonium sulphate, 10% 1,4-Dioxane

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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: 1.68→50 Å / Num. obs: 48861 / % possible obs: 100 % / Redundancy: 9.89 % / CC1/2: 0.9974 / Net I/σ(I): 21.38
Reflection shellResolution: 1.68→1.75 Å / Num. unique obs: 5694 / CC1/2: 0.9581

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPXdata processing
autoPXdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→33.42 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 2013 4.31 %
Rwork0.1716 --
obs0.1732 46724 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 22 490 3433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133011
X-RAY DIFFRACTIONf_angle_d1.1724077
X-RAY DIFFRACTIONf_dihedral_angle_d6.383410
X-RAY DIFFRACTIONf_chiral_restr0.074438
X-RAY DIFFRACTIONf_plane_restr0.009530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.21251460.1913233X-RAY DIFFRACTION100
1.72-1.770.21871460.16773156X-RAY DIFFRACTION100
1.77-1.820.21931440.1693187X-RAY DIFFRACTION100
1.82-1.880.24141460.17173213X-RAY DIFFRACTION100
1.88-1.950.22261300.183173X-RAY DIFFRACTION100
1.95-2.020.17711520.16753218X-RAY DIFFRACTION100
2.02-2.120.2211470.15833175X-RAY DIFFRACTION100
2.12-2.230.20191420.17653197X-RAY DIFFRACTION100
2.23-2.370.23121420.17633166X-RAY DIFFRACTION100
2.37-2.550.20011390.18373245X-RAY DIFFRACTION100
2.55-2.810.23381440.18463170X-RAY DIFFRACTION100
2.81-3.210.2421480.18213183X-RAY DIFFRACTION100
3.21-4.050.16561360.163218X-RAY DIFFRACTION100
4.05-33.420.20991510.16013177X-RAY DIFFRACTION100

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