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- PDB-6f83: Crystal Structure of Human Galectin-1 in Complex With Thienyl-1,2... -

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Basic information

Entry
Database: PDB / ID: 6f83
TitleCrystal Structure of Human Galectin-1 in Complex With Thienyl-1,2, 3-triazolyl Thiodigalactoside Inhibitor
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE-RECOGNITION / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN
Function / homology
Function and homology information


galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / receptor ligand activity / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / extracellular exosome / extracellular region / 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-5KT / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsCollins, P.M. / Blanchard, H.
Funding support Australia, 1items
OrganizationGrant numberCountry
Cancer Council QueenslandID1080845 Australia
CitationJournal: To be published
Title: Aromatic heterocycle galectin-1 interactions for selective single-digit nM affinity ligands
Authors: Peterson, A. / Collins, P.M. / Kahl-Knutsson, B. / Zetterberg, F.R. / Blanchard, H. / Leffler, H. / Nilsson, U.J.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2104
Polymers29,9602
Non-polymers1,2492
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-5 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.447, 58.689, 112.353
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-1 / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 14980.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09382
#2: Sugar ChemComp-5KT / 3-deoxy-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-1-thio-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranoside


Type: D-saccharide / Mass: 624.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28N6O8S3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 4-8 microlitre drops consisting of equal volumes of protein solution (20 mM sodium potassium phosphate buffer, pH 7.0, and protein at concentration of 10 mg/mL) and reservoir solution (0.2 M ...Details: 4-8 microlitre drops consisting of equal volumes of protein solution (20 mM sodium potassium phosphate buffer, pH 7.0, and protein at concentration of 10 mg/mL) and reservoir solution (0.2 M ammonium sulphate, 25% w/v polyethylene glycol 4000, 0.1M sodium acetate trihydrate, pH 6.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 30, 2009
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.199→56.18 Å / Num. obs: 14295 / % possible obs: 92 % / Redundancy: 2.9 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.078 / Rsym value: 0.064 / Net I/av σ(I): 10.8 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.2-2.321.70.4421.813790.3790.5840.44263
2.32-2.462.30.3182.417500.2420.4030.31883.2
2.46-2.633.10.2473.119830.1610.2960.24799.7
2.63-2.843.20.1564.918430.10.1870.156100
2.84-3.113.20.1057.217340.0670.1260.105100
3.11-3.483.20.06611.415680.0420.0780.066100
3.48-4.023.20.04415.613850.0290.0530.044100
4.02-4.923.20.0320.912020.020.0370.0399.8
4.92-6.953.10.03118.49180.020.0370.03199.1
6.95-52.01930.02222.95330.0150.0260.02295.3

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
PROTEUM PLUSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3OYW

3oyw


Resolution: 2.2→56.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.537 / SU ML: 0.152 / SU R Cruickshank DPI: 0.2887 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.213
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 712 5 %RANDOM
Rwork0.1708 ---
obs0.1735 13558 91.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.95 Å2 / Biso mean: 32.063 Å2 / Biso min: 8 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2---1.91 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 2.2→56.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 82 77 2249
Biso mean--55.04 35.28 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192300
X-RAY DIFFRACTIONr_bond_other_d0.0010.021535
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9963109
X-RAY DIFFRACTIONr_angle_other_deg0.87133757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265282
X-RAY DIFFRACTIONr_chiral_restr0.0810.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022535
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
LS refinement shellResolution: 2.199→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 32 -
Rwork0.254 575 -
all-607 -
obs--53.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8167-0.4648-0.49985.7255-0.15794.19860.06320.15710.0193-0.15470.01850.17640.2388-0.2022-0.08170.0275-0.0197-0.02170.06120.02130.054411.80697.815812.9686
22.5674-0.11040.68118.1811-0.38072.8295-0.0280.1601-0.13720.0477-0.04870.5369-0.2246-0.11440.07670.0203-0.0006-0.01350.08140.01750.07110.494636.759111.362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 134
2X-RAY DIFFRACTION2B1 - 134

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