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- PDB-1w6o: X-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1 COMPLEXED WITH LACTOSE -

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Basic information

Entry
Database: PDB / ID: 1w6o
TitleX-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1 COMPLEXED WITH LACTOSE
Components(GALECTIN-1) x 2
KeywordsSUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE-BINDING PROTEINS / GALACTOSIDES / GALECTIN
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
beta-lactose / BETA-MERCAPTOETHANOL / Galectin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLopez-Lucendo, M.I.F. / Gabius, H.J. / Romero, A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Growth-Regulatory Human Galectin-1: Crystallographic Characterisation of the Structural Changes Induced by Single-Site Mutations and Their Impact on the Thermodynamics of Ligand Binding
Authors: Lopez-Lucendo, M.I.F. / Solis, D. / Andre, S. / Hirabayashi, J. / Kasai, K. / Kaltner, H. / Gabius, H.J. / Romero, A.
History
DepositionAug 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)30,47010
Polymers29,2992
Non-polymers1,1718
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-5.3 kcal/mol
Surface area13970 Å2
MethodPQS
Unit cell
Length a, b, c (Å)36.712, 88.199, 93.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.37639, -0.36137, -0.85307), (-0.37068, -0.78514, 0.49614), (-0.84907, 0.50296, 0.16157)
Vector: 66.42253, 67.9696, 18.94398)

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GALECTIN-1 / BETA-GALACTOSIDE-BINDING LECTIN L-14-I / HPL / LACTOSE-BINDING LECTIN 1 / S-LAC LECTIN 1 / GALAPTIN / HBL


Mass: 14657.447 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PH14GAL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: P09382
#2: Protein GALECTIN-1 / BETA-GALACTOSIDE-BINDING LECTIN L-14-I / HPL / LACTOSE-BINDING LECTIN 1 / S-LAC LECTIN 1 / GALAPTIN / HBL


Mass: 14641.447 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PH14GAL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: P09382

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Sugars , 1 types, 2 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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

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Non-polymers , 3 types, 256 molecules

#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#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.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsMAY REGULATE CELL APOPTOSIS AND CELL DIFFERENTIATION. ENGINEERED MUTATION CYS 2 SER AND GLY 65 ASP ...MAY REGULATE CELL APOPTOSIS AND CELL DIFFERENTIATION. ENGINEERED MUTATION CYS 2 SER AND GLY 65 ASP IN CHAINS A AND B.
Sequence detailsCYS 2 ENGINEERED TO SER. GLY 65 ADDITIONAL MUTATION TO ASP

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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: 2.6 Å3/Da / Density % sol: 52.3 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: CRYSTALS WERE OBTAINED IN SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE AND 1% REMARK 280 BETA-MERCAPTO ...Details: CRYSTALS WERE OBTAINED IN SITTING DROPS BY MIXING EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) AND THE PRECIPITATING BUFFER (2M AMMONIUM SULPHATE AND 1% REMARK 280 BETA-MERCAPTO ETHANOL,PH 5.6). THE GALACTOSE COMPLEX WAS OBTAINED BY SOAKING C2S CRYSTALS FOR 72H IN THE MOTHER LIQUOR SUPPLEMENTED WITH 10 MM OF LACTOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9035
DetectorType: MARRESEACH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9035 Å / Relative weight: 1
ReflectionResolution: 1.8→24 Å / Num. obs: 28964 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZW

1gzw


Resolution: 1.9→34.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1487364.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 968 3.9 %RANDOM
Rwork0.202 ---
obs0.202 24611 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7135 Å2 / ksol: 0.372179 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å20 Å2
2---1.68 Å20 Å2
3----1.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 71 250 2380
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 151 3.8 %
Rwork0.195 3864 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SULFATO.PARAMSULFATO.TOP
X-RAY DIFFRACTION4LAC.PARAMLAC.TOP

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