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- PDB-7rgx: Crystal structure of human galectin-3 CRD in complex with Methyl ... -

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Basic information

Entry
Database: PDB / ID: 7rgx
TitleCrystal structure of human galectin-3 CRD in complex with Methyl 2-O-(2-nitrobenzoyl)-3-O-(4-methylbenzoyl)-b-D-talopyranoside
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding protein
Function / homology
Function and homology information


negative regulation of NK T cell activation / mononuclear cell migration / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / mononuclear cell migration / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / signaling receptor inhibitor activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / molecular condensate scaffold activity / mRNA processing / carbohydrate binding / protein phosphatase binding / : / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / 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
Chem-57I / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsBum-Erdene, K. / Kishor, C. / Blanchard, H.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Novel Selective Galectin-3 Antagonists Are Cytotoxic to Acute Lymphoblastic Leukemia.
Authors: Bum-Erdene, K. / Collins, P.M. / Hugo, M.W. / Tarighat, S.S. / Fei, F. / Kishor, C. / Leffler, H. / Nilsson, U.J. / Groffen, J. / Grice, I.D. / Heisterkamp, N. / Blanchard, H.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2323
Polymers15,7351
Non-polymers4972
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.260, 57.820, 61.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 15735.129 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 BL21(DE3) (bacteria) / References: UniProt: P17931
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-57I / methyl 3-O-(4-methylbenzoyl)-2-O-(2-nitrobenzoyl)-beta-D-talopyranoside


Mass: 461.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23NO10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 31% PEG 6000, 100mM MgCL2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.58→42.23 Å / Num. obs: 16853 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.7
Reflection shellResolution: 1.58→1.63 Å / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 814

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NMO

2nmo


Resolution: 1.58→30.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.013 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2273 820 5.05 %
Rwork0.1864 15418 -
all0.188 --
obs-16238 92.937 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.042 Å2-0 Å2-0 Å2
2---0.037 Å2-0 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.58→30.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 34 135 1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171197
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.6971700
X-RAY DIFFRACTIONr_angle_other_deg1.3421.6212747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2755154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3892275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61815213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6591511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2160
X-RAY DIFFRACTIONr_chiral_restr_other0.0290.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
X-RAY DIFFRACTIONr_nbd_refined0.2220.2185
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21064
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2568
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1570.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.213
X-RAY DIFFRACTIONr_nbd_other0.2770.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.214
X-RAY DIFFRACTIONr_mcbond_it1.2521.402569
X-RAY DIFFRACTIONr_mcbond_other1.2421.399568
X-RAY DIFFRACTIONr_mcangle_it1.7362.097714
X-RAY DIFFRACTIONr_mcangle_other1.7352.101715
X-RAY DIFFRACTIONr_scbond_it1.9531.69673
X-RAY DIFFRACTIONr_scbond_other1.9521.69674
X-RAY DIFFRACTIONr_scangle_it2.9792.452977
X-RAY DIFFRACTIONr_scangle_other2.9782.453978
X-RAY DIFFRACTIONr_lrange_it4.27917.6481313
X-RAY DIFFRACTIONr_lrange_other4.27517.6221313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.58-1.6210.265420.2477480.24812640.8860.90362.50.23
1.621-1.6650.265410.2368280.23812330.890.89870.47850.216
1.665-1.7130.298490.2218910.22512100.8740.90477.6860.2
1.713-1.7660.217620.21110000.21111590.9140.92191.63070.186
1.766-1.8240.219610.2110680.2111400.9240.92599.03510.188
1.824-1.8870.241610.20810220.2110860.9180.92999.72380.191
1.887-1.9580.224590.19510030.19710650.9220.93499.71830.181
1.958-2.0380.285540.1969650.20110210.9170.93599.80410.186
2.038-2.1280.233480.2049330.2069840.9220.93199.69510.196
2.128-2.2320.288430.1998970.2029430.8920.93499.68190.192
2.232-2.3520.241480.1998530.2019010.9220.9351000.195
2.352-2.4930.226500.1778050.188560.9330.95199.88320.178
2.493-2.6640.243370.1727690.1758070.9250.95699.87610.175
2.664-2.8760.206310.1727240.1747550.9410.9521000.178
2.876-3.1480.253280.1796680.1826960.9340.9471000.191
3.148-3.5150.171300.1746150.1746450.9620.9561000.192
3.515-4.050.199240.1625380.1645620.960.9631000.181
4.05-4.9390.191250.1454730.1474980.9580.9751000.167
4.939-6.8980.222200.1933760.1953960.9640.961000.219
6.898-30.960.19970.2142420.2132500.9530.95999.60.256

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