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- PDB-6f2q: Neutron crystal structure of perdeuterated galectin-3C in the lig... -

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Basic information

Entry
Database: PDB / ID: 6f2q
TitleNeutron crystal structure of perdeuterated galectin-3C in the ligand-free form
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 / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration / 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 / regulation of T cell proliferation / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / RNA splicing / neutrophil chemotaxis / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma 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. / 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: 1.03 Å
AuthorsManzoni, F. / Blakeley, M.P. / Oksanen, E. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Spallation Source 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 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / diffrn_detector / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 1, 2024Group: 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-3


Theoretical massNumber of molelcules
Total (without water)15,7011
Polymers15,7011
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.390, 58.620, 64.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 15701.049 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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 %
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 THEN INTRODUCED. THE DROP WAS FED WITH FRESH PROTEIN BY ADDING 3-4 MICROLITRES OF PROTEIN WITH 10 MM LACTOSE EVERY 3-4 DAYS FOR 3 MONTHS. LACTOSE WAS THEN REMOVED IN TWO STEPS, FIRST BY DIALYSING AGAINST 1M GLYCEROL FOR 1 MONTH THEN AGAINST BUFFER WITH NO GLYCEROL FOR 1 MONTH. FOR DETAILS, SEE MANZONI ET AL. (2016).

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.98081
NUCLEAR REACTORILL LADI III23.35-4.35
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDMar 10, 2017FOCUSING MIRRORS
2IMAGE PLATEFeb 15, 2017
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.980811
23.351
34.351
Reflection

Entry-ID: 6F2Q

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)Rsym value
1.03-287017399.81410.0440.012135.5
1.8-30984483.84.90.9930.05328.50.132
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
1.03-1.069.32.357151380.3550.933199.2
1.8-1.93.40.19411770.9170.091267.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
LAUEGENdata scaling
PHENIXphasing
Refinement

SU ML: 0.11 / Cross valid method: THROUGHOUT / Method to determine structure: FOURIER SYNTHESIS / Phase error: 13.66 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 6EYM

6eym

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
1.03-29.31X-RAY DIFFRACTION0.15410.13730.13844369701656.2399.821.35
1.757-28.094NEUTRON DIFFRACTION0.21070.17150.1741735117856.2480.83
Refinement stepCycle: LAST / Resolution: 1.03→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 0 59 1167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112561
X-RAY DIFFRACTIONf_angle_d1.434539
X-RAY DIFFRACTIONf_dihedral_angle_d16.358716
X-RAY DIFFRACTIONf_chiral_restr0.107188
X-RAY DIFFRACTIONf_plane_restr0.009379
NEUTRON DIFFRACTIONf_bond_d0.0112561
NEUTRON DIFFRACTIONf_angle_d1.434539
NEUTRON DIFFRACTIONf_dihedral_angle_d16.358716
NEUTRON DIFFRACTIONf_chiral_restr0.107188
NEUTRON DIFFRACTIONf_plane_restr0.009379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.04170.3451450.352180X-RAY DIFFRACTION99
1.0417-1.0540.3351400.30152117X-RAY DIFFRACTION99
1.054-1.06680.26491440.27272172X-RAY DIFFRACTION99
1.0668-1.08030.25641430.23322141X-RAY DIFFRACTION100
1.0803-1.09460.23171430.20682154X-RAY DIFFRACTION99
1.0946-1.10950.18181450.19222179X-RAY DIFFRACTION99
1.1095-1.12540.1841440.18362176X-RAY DIFFRACTION100
1.1254-1.14220.20751430.18142152X-RAY DIFFRACTION100
1.1422-1.160.21861450.20372182X-RAY DIFFRACTION100
1.16-1.17910.16821430.16892158X-RAY DIFFRACTION100
1.1791-1.19940.16831450.15142185X-RAY DIFFRACTION100
1.1994-1.22120.14281440.1352164X-RAY DIFFRACTION100
1.2212-1.24470.1321460.12672203X-RAY DIFFRACTION100
1.2447-1.27010.13491430.12292139X-RAY DIFFRACTION100
1.2701-1.29770.13441460.11622201X-RAY DIFFRACTION100
1.2977-1.32790.15311430.12442181X-RAY DIFFRACTION100
1.3279-1.36110.12911440.12632189X-RAY DIFFRACTION100
1.3611-1.39790.16751460.12762193X-RAY DIFFRACTION100
1.3979-1.43910.14871460.12772172X-RAY DIFFRACTION100
1.4391-1.48550.14081480.11352193X-RAY DIFFRACTION100
1.4855-1.53860.13821450.1122194X-RAY DIFFRACTION100
1.5386-1.60020.13351460.10792189X-RAY DIFFRACTION100
1.6002-1.6730.12131450.11482210X-RAY DIFFRACTION100
1.673-1.76120.11971480.11662218X-RAY DIFFRACTION100
1.7612-1.87150.14831480.11752215X-RAY DIFFRACTION100
1.8715-2.0160.13891460.1132220X-RAY DIFFRACTION100
2.016-2.21880.13951470.12292225X-RAY DIFFRACTION100
2.2188-2.53970.14661480.14242251X-RAY DIFFRACTION100
2.5397-3.19920.18331520.15932272X-RAY DIFFRACTION100
3.1992-29.32190.14731580.13082371X-RAY DIFFRACTION99
1.757-1.89260.27271080.25051749NEUTRON DIFFRACTION65
1.8926-2.08310.24731260.18762011NEUTRON DIFFRACTION75
2.0831-2.38430.20771580.16812193NEUTRON DIFFRACTION82
2.3843-3.00350.23531620.17752400NEUTRON DIFFRACTION88
3.0035-28.09790.19141810.15982697NEUTRON DIFFRACTION94

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