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- PDB-6exy: Neutron crystal structure of perdeuterated galectin-3C in complex... -

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Basic information

Entry
Database: PDB / ID: 6exy
TitleNeutron crystal structure of perdeuterated galectin-3C in complex with glycerol
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / galectin / hydrogen bonding / molecular recognition / perdeuteration
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / positive chemotaxis / macrophage chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / molecular condensate scaffold activity / neutrophil chemotaxis / RNA splicing / secretory granule membrane / positive regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / mRNA processing / carbohydrate binding / collagen-containing extracellular matrix / protein phosphatase binding / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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 / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / FOURIER SYNTHESIS / Resolution: 1.1 Å
AuthorsManzoni, F. / Schrader, T.E. / Ostermann, A. / Oksanen, E. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Sweden
Citation
Journal: J. Med. Chem. / Year: 2018
Title: Elucidation of Hydrogen Bonding Patterns in Ligand-Free, Lactose- and Glycerol-Bound Galectin-3C by Neutron Crystallography to Guide Drug Design.
Authors: Manzoni, F. / Wallerstein, J. / Schrader, T.E. / Ostermann, A. / Coates, L. / Akke, M. / Blakeley, M.P. / Oksanen, E. / Logan, D.T.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C.
Authors: Manzoni, F. / Saraboji, K. / Sprenger, J. / Kumar, R. / Noresson, A.L. / Nilsson, U.J. / Leffler, H. / Fisher, S.Z. / Schrader, T.E. / Ostermann, A. / Coates, L. / Blakeley, M.P. / Oksanen, E. / Logan, D.T.
History
DepositionNov 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9242
Polymers15,8321
Non-polymers921
Water1,820101
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-0 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.314, 58.352, 63.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Galectin-3 / / Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / ...Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / Galactoside-binding protein / GALBP / IgE-binding protein / L-31 / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 15832.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 44 % / Description: Volume approximately 1.0 mm3
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12-15% PEG 4000 OR PEG 3000, 0.1M MGCL2, 0.015M BETA MERCAPTOETHANOL, 0.1M TRIS-DCL, PD 7.9, 0.4M NaSCN. All dissolved in D2O. Crystal grown in a 15 + 15 microlitre sitting drop that was ...Details: 12-15% PEG 4000 OR PEG 3000, 0.1M MGCL2, 0.015M BETA MERCAPTOETHANOL, 0.1M TRIS-DCL, PD 7.9, 0.4M NaSCN. All dissolved in D2O. Crystal grown in a 15 + 15 microlitre sitting drop that was first equilibrated for 1 week. A small crystal grown at 20-28% PEG was introduced. The drop was fed with fresh protein by adding 3-4 micro litres of protein with 10 mM lactose every 3-4 days for 3 months. Then the lactose was exchanged for glycerol by dialysis for at least one month against 10% glycerol (1.37 M), 24% PEG 4000 in the same buffer. For details see Manzoni et al. (2016).

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22981
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONMAX II I911-311
NUCLEAR REACTORFRM II BEAMLINE BIODIFF22.67
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMay 15, 2016
BIODIFF2IMAGE PLATENov 1, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2PG(002)
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.671
Reflection

Biso Wilson estimate: 11.45 Å2 / Entry-ID: 6EXY

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
1.1-43.1544149512.310.0680.02120.2
1.65-28.21659294.73.10.1350.08725.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allDiffraction-ID% possible allNum. unique obs
1.1-1.1271.2591.40.7260.543191.5
1.65-1.712.60.4991.62901544

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
XDSdata reduction
Aimlessdata scaling
PHENIX1.13_2998phasing
Refinement

SU ML: 0.0845 / Cross valid method: FREE R-VALUE / Method to determine structure: FOURIER SYNTHESIS / Phase error: 14.161 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Starting model: 3ZSJ

3zsj

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.1-31.93X-RAY DIFFRACTION15.310.13730.12310.12392751543475.0694.7911.34
1.7-28.2NEUTRON DIFFRACTION0.18730.15020.1522782151785.1595.32
Refinement stepCycle: LAST / Resolution: 1.1→31.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 6 101 1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972691
X-RAY DIFFRACTIONf_angle_d1.73514674
X-RAY DIFFRACTIONf_chiral_restr0.1292190
X-RAY DIFFRACTIONf_plane_restr0.0081386
X-RAY DIFFRACTIONf_dihedral_angle_d17.6582730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.120.22151280.25532431X-RAY DIFFRACTION91.16
1.12-1.140.24911170.24072466X-RAY DIFFRACTION91.5
1.14-1.160.24631430.22222448X-RAY DIFFRACTION91.55
1.16-1.180.25061320.21462470X-RAY DIFFRACTION92.6
1.18-1.210.19961450.20162499X-RAY DIFFRACTION92.42
1.21-1.240.21211280.18692506X-RAY DIFFRACTION92.88
1.24-1.270.21341170.16842502X-RAY DIFFRACTION93.3
1.27-1.30.15011530.14682526X-RAY DIFFRACTION94
1.3-1.340.18391340.14312532X-RAY DIFFRACTION93.71
1.34-1.390.14481230.13442575X-RAY DIFFRACTION94.01
1.39-1.440.13441540.12312526X-RAY DIFFRACTION94.97
1.44-1.490.14461260.1052598X-RAY DIFFRACTION95.41
1.49-1.560.11981460.09652597X-RAY DIFFRACTION95.91
1.56-1.640.1081380.09972623X-RAY DIFFRACTION96.34
1.64-1.750.1181210.09582637X-RAY DIFFRACTION96.37
1.75-1.880.11491360.09882671X-RAY DIFFRACTION96.83
1.88-2.070.10151630.0952646X-RAY DIFFRACTION97.4
2.07-2.370.13511410.10462711X-RAY DIFFRACTION98.24
2.37-2.990.14231500.12292764X-RAY DIFFRACTION98.78
2.99-31.930.11871560.11632868X-RAY DIFFRACTION97.9

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