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- PDB-1gan: COMPLEX OF TOAD OVARY GALECTIN WITH N-ACETYLGALACTOSE -

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Basic information

Entry
Database: PDB / ID: 1gan
TitleCOMPLEX OF TOAD OVARY GALECTIN WITH N-ACETYLGALACTOSE
ComponentsGALECTIN-1
KeywordsS-LECTIN / CARBOHYDRATE BINDING / LECTIN
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
N-acetyl-alpha-lactosamine / Galectin-1
Similarity search - Component
Biological speciesBufo arenarum (Argentine toad)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 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.R. / Amzel, L.M.
History
DepositionNov 6, 1996Processing site: BNL
Revision 1.0Sep 4, 1997Provider: 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 / Database references / Derived calculations / 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 / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,1624
Polymers29,3952
Non-polymers7672
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.330, 54.330, 186.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.810039, -0.423742, 0.405315), (-0.39106, -0.124668, -0.911883), (0.436932, -0.897163, -0.064723)
Vector: 57.8852, 106.9261, 77.5613)

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Components

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


Mass: 14697.648 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-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
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 grow
*PLUS
Method: vapor diffusion
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-12 mg/mlprotein1drop
25 mMLacNAc1drop
356 %satammonium sulfate1reservoir
4100 mMTris-acetate1reservoirpH6.6
51 %2-methyl-2,4-pentanediol1reservoir
61 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / 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: 2.23→30 Å / Num. obs: 13192 / % possible obs: 90.9 % / Observed criterion σ(I): 0.5 / Redundancy: 7.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 10000
Reflection shellResolution: 2.25→2.5 Å / Redundancy: 7.49 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.19 / % possible all: 73.1
Reflection
*PLUS
Num. all: 13192 / Num. obs: 11873 / % possible obs: 901 %
Reflection shell
*PLUS
% possible obs: 73.1 % / Rmerge(I) obs: 0.19

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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 1SLT

1slt


Resolution: 2.23→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.1831 --
obs0.1831 11870 87.23 %
Displacement parametersBiso mean: 33.31 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.23→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 52 30 2152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.498
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.23→2.33 Å
RfactorNum. reflection% reflection
Rwork0.2234 581 -
obs--52.52 %
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
Refinement
*PLUS
Rfactor Rfree: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.44

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