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- PDB-8b0z: Galectin-1 in Complex with Ligand JM171 -

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Basic information

Entry
Database: PDB / ID: 8b0z
TitleGalectin-1 in Complex with Ligand JM171
Components(Galectin-1) x 2
KeywordsPROTEIN BINDING / Gal-1 / Galectin / Lectin
Function / homology
Function and homology information


galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / myoblast differentiation / plasma cell differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / myoblast differentiation / plasma cell differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / : / regulation of apoptotic process / positive regulation of viral entry into host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / receptor ligand activity / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / 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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-OV6 / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsGrimm, C. / Mut, J. / Seibel, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)326998133 Germany
CitationJournal: To Be Published
Title: Galectin-1 in Complex with Ligand JM171
Authors: Grimm, C. / Mut, J. / Seibel, J.
History
DepositionSep 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6536
Polymers29,4372
Non-polymers1,2154
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.246, 58.306, 111.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#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: 14680.636 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: 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: 14756.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382

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Non-polymers , 4 types, 229 molecules

#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-OV6 / ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-4-[(1-methyl-1,2,3-triazol-4-yl)methoxy]-3,5-bis(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-2-propoxy-oxan-3-yl]ethanamide


Mass: 520.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N4O11 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2.20 ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.23→40.32 Å / Num. obs: 80915 / % possible obs: 98.57 % / Redundancy: 12.5 % / Biso Wilson estimate: 15.88 Å2 / CC1/2: 0.997 / Net I/σ(I): 22.55
Reflection shellResolution: 1.233→1.277 Å / Num. unique obs: 6953 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mwx

5mwx


Resolution: 1.23→40.32 Å / SU ML: 0.148 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2235 2000 2.47 %
Rwork0.2008 78864 -
obs0.2013 80864 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 1.23→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 81 225 2361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412335
X-RAY DIFFRACTIONf_angle_d1.57383185
X-RAY DIFFRACTIONf_chiral_restr0.0989351
X-RAY DIFFRACTIONf_plane_restr0.0105424
X-RAY DIFFRACTIONf_dihedral_angle_d11.3931449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.260.28021150.35034532X-RAY DIFFRACTION80.75
1.26-1.30.30941430.28715647X-RAY DIFFRACTION99.78
1.3-1.340.30831430.27375627X-RAY DIFFRACTION99.95
1.34-1.380.24051430.25135641X-RAY DIFFRACTION99.93
1.38-1.430.24921440.24325686X-RAY DIFFRACTION99.95
1.43-1.490.24721430.23175644X-RAY DIFFRACTION99.95
1.49-1.550.23821440.24075658X-RAY DIFFRACTION99.88
1.55-1.640.23381440.2325667X-RAY DIFFRACTION99.78
1.64-1.740.26391440.23765708X-RAY DIFFRACTION99.93
1.74-1.870.26351450.2225710X-RAY DIFFRACTION100
1.87-2.060.23551460.20825733X-RAY DIFFRACTION100
2.06-2.360.20591440.19225740X-RAY DIFFRACTION99.93
2.36-2.970.22891480.19595817X-RAY DIFFRACTION99.98
2.97-40.320.19591540.16896054X-RAY DIFFRACTION99.9

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