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- PDB-1a78: COMPLEX OF TOAD OVARY GALECTIN WITH THIO-DIGALACTOSE -

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Basic information

Entry
Database: PDB / ID: 1a78
TitleCOMPLEX OF TOAD OVARY GALECTIN WITH THIO-DIGALACTOSE
ComponentsGALECTIN-1
KeywordsLECTIN / S-LECTIN / CARBOHYDRATE BINDING / COMPLEX (LECTIN-SACCHARIDE)
Function / homology
Function and homology information


carbohydrate binding / extracellular region
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
thiodigalactoside / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Galectin-1
Similarity search - Component
Biological speciesBufo arenarum (Argentine toad)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAmzel, L.M. / Bianchet, M.A. / Ahmed, H. / Vasta, G.R.
CitationJournal: Proteins / Year: 2000
Title: Soluble beta-galactosyl-binding lectin (galectin) from toad ovary: crystallographic studies of two protein-sugar complexes
Authors: Bianchet, M.A. / Ahmed, H. / Vasta, G. / Amzel, L.M.
History
DepositionMar 20, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / 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_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.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.process_site / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 12, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_branch_scheme / pdbx_molecule_features / struct_conn
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 / _chem_comp.pdbx_synonyms / _pdbx_branch_scheme.pdb_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id
Revision 3.1Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)30,3225
Polymers29,4512
Non-polymers8713
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.800, 51.000, 56.300
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.606149, 0.675442, -0.419954), (0.684481, -0.711912, -0.15706), (-0.405055, -0.192248, -0.893852)
Vector: 6.6742, -7.6792, 14.5858)

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Components

#1: Protein GALECTIN-1 / / S-LECTIN GALECTIN


Mass: 14725.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bufo arenarum (Argentine toad) / Organ: OVARY / References: UniProt: P56217
#2: Polysaccharide beta-D-galactopyranose-(1-1)-1-thio-beta-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 358.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides, and with reducing-end-to-reducing-end glycosidic bond
References: thiodigalactoside
DescriptorTypeProgram
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Galp1SH]{[(1+S)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growpH: 6.6
Details: DROPS OF EQUAL AMOUNT OF 10-12 MG/ML PROTEIN AND RESERVOIR SOLUTION WERE EQUILIBRATED AGAINST 1 ML OF (NH4)2SO4 AT 56% SATURATION IN 100MM TRIS-ACETATE BUFFER, PH 6.6 AND 1% MPD AND 1% DTT
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-12 mg/mlprotein1drop
256 %satammonium sulfate1reservoir
3100 mMTris-acetate1reservoirpH6.6
41 %MPD1reservoir
51 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MONOCHROMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.945→15 Å / Num. obs: 14540 / % possible obs: 68.6 % / Observed criterion σ(I): 0.5 / Redundancy: 2.3 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086
Reflection
*PLUS
Num. measured all: 32134

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISV. 3.4data reduction
R-AXISV 3.4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAN

1gan


Resolution: 2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1550 10 %RANDOM
Rwork0.194 ---
obs0.194 15569 81.5 %-
Displacement parametersBiso mean: 36.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 54 46 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.739
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.12
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.821.5
X-RAY DIFFRACTIONx_mcangle_it3.132
X-RAY DIFFRACTIONx_scbond_it2.722
X-RAY DIFFRACTIONx_scangle_it3.942.5
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2578 82 3.46 %
Rwork0.2869 769 -
obs--36 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.12
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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