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- PDB-8hl9: Crystal structure of Galectin-8 C-CRD with part of linker -

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Basic information

Entry
Database: PDB / ID: 8hl9
TitleCrystal structure of Galectin-8 C-CRD with part of linker
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / Binding sugar / Immunological function / Linker
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / extracellular space / membrane / cytoplasm / 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: 1.6 Å
AuthorsSi, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82201916 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Linker remodels human Galectin-8 structure and regulates its hemagglutination and pro-apoptotic activity.
Authors: Si, Y. / Cai, J. / Zhu, J. / Wang, Y. / Zhang, F. / Meng, L. / Huang, J. / Shi, A.
History
DepositionNov 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-8


Theoretical massNumber of molelcules
Total (without water)16,7131
Polymers16,7131
Non-polymers00
Water2,504139
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)52.900, 52.900, 126.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 16713.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes pH 7.0, 0.2M MgCl2, 30% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.6→19.62 Å / Num. obs: 24410 / % possible obs: 99.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 1173

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
Aimlessdata scaling
XDSdata reduction
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.62 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 1979 8.23 %
Rwork0.2135 --
obs0.2166 24059 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 0 139 1275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071161
X-RAY DIFFRACTIONf_angle_d0.911566
X-RAY DIFFRACTIONf_dihedral_angle_d6.788152
X-RAY DIFFRACTIONf_chiral_restr0.063170
X-RAY DIFFRACTIONf_plane_restr0.01203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.261390.22591551X-RAY DIFFRACTION100
1.64-1.680.24921410.22481564X-RAY DIFFRACTION100
1.68-1.730.30121420.22311583X-RAY DIFFRACTION100
1.73-1.790.24871410.21721581X-RAY DIFFRACTION100
1.79-1.850.28781420.24041570X-RAY DIFFRACTION100
1.85-1.930.32091370.31261549X-RAY DIFFRACTION97
1.93-2.020.32931310.29841472X-RAY DIFFRACTION92
2.02-2.120.25111420.21241582X-RAY DIFFRACTION100
2.12-2.250.26371240.25781380X-RAY DIFFRACTION87
2.25-2.430.2761420.20791588X-RAY DIFFRACTION99
2.43-2.670.26051460.21511625X-RAY DIFFRACTION100
2.67-3.060.29931460.20961619X-RAY DIFFRACTION100
3.06-3.850.20061490.18161663X-RAY DIFFRACTION99
3.85-19.620.21681570.18971753X-RAY DIFFRACTION99

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