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- PDB-6ljp: Crystal structure of human galectin-16 -

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Basic information

Entry
Database: PDB / ID: 6ljp
TitleCrystal structure of human galectin-16
ComponentsGalectin-16
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


lactose binding / positive regulation of T cell apoptotic process / carbohydrate binding / apoptotic process
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSu, J.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Human galectin-16 has a pseudo ligand binding site and plays a role in regulating c-Rel-mediated lymphocyte activity.
Authors: Si, Y. / Yao, Y. / Jaramillo Ayala, G. / Li, X. / Han, Q. / Zhang, W. / Xu, X. / Tai, G. / Mayo, K.H. / Zhou, Y. / Su, J.
History
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-16


Theoretical massNumber of molelcules
Total (without water)16,8761
Polymers16,8761
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7270 Å2
Unit cell
Length a, b, c (Å)56.096, 34.797, 68.066
Angle α, β, γ (deg.)90.000, 101.280, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-289-

HOH

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Components

#1: Protein Galectin-16


Mass: 16876.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS16 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MUM7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→19.44 Å / Num. obs: 8628 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.188 / Num. unique obs: 669

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XRH

5xrh


Resolution: 2→19.44 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2418 861 9.99 %
Rwork0.1904 --
obs0.1954 8622 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.01 Å2 / Biso mean: 13.8453 Å2 / Biso min: 3.56 Å2
Refinement stepCycle: final / Resolution: 2→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 0 137 1278
Biso mean---21.01 -
Num. residues----139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.130.27441440.1971294143897
2.13-2.290.28331360.23261233136993
2.29-2.520.29351440.22151295143998
2.52-2.880.28391420.22071289143198
2.88-3.630.23431470.17541319146698
3.63-19.440.17631480.15591331147997

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