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- PDB-4q26: Crystal Structure of Galectin-1 in Complex with N-Acetyllactosamine -

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Basic information

Entry
Database: PDB / ID: 4q26
TitleCrystal Structure of Galectin-1 in Complex with N-Acetyllactosamine
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...galectin complex / lactose binding / plasma cell differentiation / galactoside binding / 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) / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / extracellular exosome / extracellular region / 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
N-acetyl-alpha-lactosamine / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsGrimm, C. / Bertleff-Zieschang, N.
CitationJournal: To be Published
Title: Crystal Structure of Galectin-1 in Complex with N-Acetyllactosamine
Authors: Grimm, C. / Bertleff-Zieschang, N.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
G: Galectin-1
H: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6909
Polymers60,0644
Non-polymers1,6255
Water8,917495
1
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7994
Polymers30,0322
Non-polymers7672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Galectin-1
H: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8915
Polymers30,0322
Non-polymers8593
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3992
Polymers15,0161
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3992
Polymers15,0161
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
G: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4923
Polymers15,0161
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
H: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3992
Polymers15,0161
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.384, 85.517, 116.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-399-

HOH

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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: 15016.079 Da / Num. of mol.: 4
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: Polysaccharide
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.399→48.023 Å / Num. all: 129682 / Num. obs: 129682 / % possible obs: 99.2 % / Observed criterion σ(I): 16.7 / Rsym value: 0.092
Reflection shellHighest resolution: 1.399 Å

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.399→48.023 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 2000 1.54 %
Rwork0.1623 --
obs0.1629 129632 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.457 Å2 / ksol: 0.433 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4856 Å20 Å2-0 Å2
2--4.4418 Å2-0 Å2
3----1.9562 Å2
Refinement stepCycle: LAST / Resolution: 1.399→48.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 110 495 4729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184519
X-RAY DIFFRACTIONf_angle_d2.0236158
X-RAY DIFFRACTIONf_dihedral_angle_d19.8271696
X-RAY DIFFRACTIONf_chiral_restr0.132689
X-RAY DIFFRACTIONf_plane_restr0.01819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.399-1.43380.39761370.36568733X-RAY DIFFRACTION96
1.4338-1.47250.33421430.28369130X-RAY DIFFRACTION100
1.4725-1.51590.26841420.24429063X-RAY DIFFRACTION100
1.5159-1.56480.23331430.29105X-RAY DIFFRACTION100
1.5648-1.62070.24841430.17299140X-RAY DIFFRACTION100
1.6207-1.68560.22571420.15749075X-RAY DIFFRACTION100
1.6856-1.76240.22251430.14429147X-RAY DIFFRACTION100
1.7624-1.85530.18161440.13299153X-RAY DIFFRACTION100
1.8553-1.97150.17571430.12419163X-RAY DIFFRACTION100
1.9715-2.12370.17521440.12459184X-RAY DIFFRACTION100
2.1237-2.33750.20471440.12689190X-RAY DIFFRACTION100
2.3375-2.67570.18451460.14959270X-RAY DIFFRACTION100
2.6757-3.37090.1731450.14839315X-RAY DIFFRACTION100
3.3709-48.05110.20631410.18098964X-RAY DIFFRACTION93

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