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- PDB-6m5y: Structure of human galectin-1 tandem-repeat mutant with lactose -

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Basic information

Entry
Database: PDB / ID: 6m5y
TitleStructure of human galectin-1 tandem-repeat mutant with lactose
ComponentsGalectin-1,Galectin-1
KeywordsSUGAR BINDING PROTEIN / Lectin / Beta-Sandwich / Apoptosis / Immune Regulation
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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-lactose / alpha-lactose / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsNonaka, Y. / Kamitori, S. / Nakamura, T.
CitationJournal: Glycobiology / Year: 2021
Title: Crystal structure and conformational stability of a galectin-1 tandem-repeat mutant with a short linker.
Authors: Nonaka, Y. / Ogawa, T. / Shoji, H. / Nishi, N. / Kamitori, S. / Nakamura, T.
History
DepositionMar 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 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-1,Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0673
Polymers29,3831
Non-polymers6852
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint4 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.380, 95.640, 37.630
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
11A-500-

HOH

21A-514-

HOH

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Components

#1: Protein Galectin-1,Galectin-1


Mass: 29382.717 Da / Num. of mol.: 1 / Mutation: C3/17/61/89/131S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09382
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20%(w/v) PEG3350, 200 mM Ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→47.87 Å / Num. obs: 50739 / % possible obs: 99.6 % / Redundancy: 6.21 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.08
Reflection shellResolution: 1.38→1.416 Å / Num. unique obs: 3679 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model structure obtained using SWISS-MODEL and 1GZW

1gzw


Resolution: 1.38→47.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.942 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21902 2571 5.1 %RANDOM
Rwork0.18324 ---
obs0.1851 48114 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.368 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å2-0 Å2
2---2.17 Å20 Å2
3---3.98 Å2
Refinement stepCycle: 1 / Resolution: 1.38→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 46 211 2317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192193
X-RAY DIFFRACTIONr_bond_other_d0.0040.022041
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9762986
X-RAY DIFFRACTIONr_angle_other_deg0.96534718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2445283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01925.048105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84515345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6291511
X-RAY DIFFRACTIONr_chiral_restr0.1130.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212541
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02514
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7581.8931093
X-RAY DIFFRACTIONr_mcbond_other3.75858.2781092
X-RAY DIFFRACTIONr_mcangle_it4.642.8511368
X-RAY DIFFRACTIONr_mcangle_other4.67458.1571369
X-RAY DIFFRACTIONr_scbond_it5.7452.2641100
X-RAY DIFFRACTIONr_scbond_other5.7432.5351100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7523.3651612
X-RAY DIFFRACTIONr_long_range_B_refined5.9492385
X-RAY DIFFRACTIONr_long_range_B_other5.9762295
X-RAY DIFFRACTIONr_rigid_bond_restr9.4332193
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded18.36552139
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 176 -
Rwork0.315 3499 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 12.322 Å / Origin y: 25.647 Å / Origin z: 11.803 Å
111213212223313233
T0.0462 Å20.0004 Å20.0004 Å2-0.0124 Å20.0006 Å2--0.0463 Å2
L0.0031 °2-0.0075 °20.0081 °2-0.0301 °2-0.0324 °2--0.0354 °2
S0.0005 Å °0.0011 Å °-0.0071 Å °-0.0109 Å °-0.0009 Å °0.0015 Å °0.0093 Å °0.0028 Å °0.0003 Å °

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