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- PDB-7rh4: Co-crystallization of human galectin-3 CRD complex with Methyl 2-... -

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Basic information

Entry
Database: PDB / ID: 7rh4
TitleCo-crystallization of human galectin-3 CRD complex with Methyl 2-O-(2-nitro-4-fluoro)-benzoyl-3-O-toluoyl-b-D-talopyranoside
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Carbohydrates-binding protein
Function / homology
Function and homology information


negative regulation of NK T cell activation / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / 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 / 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 / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / signaling receptor inhibitor activity / 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 / immunological synapse / ficolin-1-rich granule membrane / laminin binding / neutrophil chemotaxis / epithelial cell differentiation / 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 / 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
Chem-5A4 / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.201 Å
AuthorsCollins, P.M. / 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 16, 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

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2503
Polymers15,7351
Non-polymers5152
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.933, 57.929, 62.067
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-5A4 / methyl 2-O-(4-fluoro-2-nitrobenzoyl)-3-O-(4-methylbenzoyl)-beta-D-talopyranoside


Mass: 479.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22FNO10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 31% PEG 6000, 100mM MgCl2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.2→42.35 Å / Num. obs: 38453 / % possible obs: 93.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.4
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 952

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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: 1.201→42.349 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.65 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1642 1856 4.834 %
Rwork0.1538 36542 -
all0.154 --
obs-38398 93.251 %
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: 11.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.156 Å2-0 Å20 Å2
2---0.122 Å20 Å2
3----0.034 Å2
Refinement stepCycle: LAST / Resolution: 1.201→42.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 35 219 1363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131246
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171198
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.6371700
X-RAY DIFFRACTIONr_angle_other_deg1.4371.6092752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8775152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65221.54971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85615214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7011511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2159
X-RAY DIFFRACTIONr_chiral_restr_other0.020.23
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021525
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02310
X-RAY DIFFRACTIONr_nbd_refined0.2150.2177
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.21097
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2576
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2676
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2120
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0630.27
X-RAY DIFFRACTIONr_nbd_other0.1770.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3640.234
X-RAY DIFFRACTIONr_mcbond_it0.9330.941590
X-RAY DIFFRACTIONr_mcbond_other0.9260.939589
X-RAY DIFFRACTIONr_mcangle_it1.3261.414748
X-RAY DIFFRACTIONr_mcangle_other1.3281.415749
X-RAY DIFFRACTIONr_scbond_it2.0161.194656
X-RAY DIFFRACTIONr_scbond_other2.0031.191653
X-RAY DIFFRACTIONr_scangle_it2.9891.717952
X-RAY DIFFRACTIONr_scangle_other2.9851.717952
X-RAY DIFFRACTIONr_lrange_it4.75513.3081324
X-RAY DIFFRACTIONr_lrange_other4.75313.3171325
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
1.201-1.2320.317750.27815990.27929960.7760.83455.87450.26
1.232-1.2660.2551050.25120080.25129270.8680.86272.190.229
1.266-1.3020.241350.22822440.22928270.9020.90284.15280.2
1.302-1.3420.2481410.22524600.22627610.890.91194.2050.193
1.342-1.3860.2311200.20125700.20327000.9330.93499.62960.167
1.386-1.4350.1991130.18424860.18526000.9410.95199.96150.148
1.435-1.4890.1821050.16324090.16325160.9540.9699.92050.131
1.489-1.550.1581340.15722800.15724180.9660.96599.83460.127
1.55-1.6190.1711060.1522150.15123250.9640.96799.8280.124
1.619-1.6980.1791050.13621160.13822210.9630.9691000.113
1.698-1.7890.1431180.14520080.14521270.9710.96899.9530.123
1.789-1.8980.1691050.13419110.13620160.9710.9761000.117
1.898-2.0280.145910.13518050.13618960.9760.9771000.123
2.028-2.190.156900.13716770.13817670.9750.9781000.126
2.19-2.3990.146920.12715670.12816590.9820.9831000.118
2.399-2.6810.13580.1314260.1314850.980.9899.93270.125
2.681-3.0930.137580.13412850.13413430.9760.9771000.131
3.093-3.7840.128420.13510950.13511370.9820.9781000.141
3.784-5.330.128420.148630.149090.9860.98499.560.154
5.33-42.3490.317210.2555180.2575470.9290.96598.53750.267

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