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- PDB-6ljq: human galectin-16 R55N -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6ljq
Titlehuman galectin-16 R55N
ComponentsGalectin-16
KeywordsSUGAR BINDING PROTEIN / human galectin-16 R55N
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
beta-lactose / Galectin-16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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

Downloads & links

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Assembly

Deposited unit
A: Galectin-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1762
Polymers16,8331
Non-polymers3421
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint5 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.817, 34.333, 67.892
Angle α, β, γ (deg.)90.000, 102.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Galectin-16


Mass: 16833.281 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: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.89 Å3/Da / Density % sol: 34.91 %
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: 1.49→19.27 Å / Num. obs: 20576 / % possible obs: 99.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.4
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.461 / Num. unique obs: 978

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LJP

6ljp


Resolution: 1.49→19.27 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2083 1991 9.68 %
Rwork0.1756 --
obs0.1787 20568 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.15 Å2 / Biso mean: 23.5566 Å2 / Biso min: 12.81 Å2
Refinement stepCycle: final / Resolution: 1.49→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 23 133 1298
Biso mean--31.56 32.94 -
Num. residues----140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.530.32841340.31221276141099
1.53-1.570.34051330.27171326145998
1.57-1.610.27661480.23181325147399
1.61-1.670.27771410.21851307144899
1.67-1.730.24581310.19671340147199
1.73-1.80.23261540.192313071461100
1.8-1.880.22381420.18661315145799
1.88-1.980.21561410.180813211462100
1.98-2.10.23681480.16911324147299
2.1-2.260.19371400.16751345148599
2.26-2.490.25651470.17861322146999
2.49-2.850.20221410.18691349149099
2.85-3.580.18241410.16841335147698
3.58-19.270.16941500.14761385153599

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