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- PDB-1slt: STRUCTURE OF S-LECTIN, A DEVELOPMENTALLY REGULATED VERTEBRATE BET... -

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Basic information

Entry
Database: PDB / ID: 1slt
TitleSTRUCTURE OF S-LECTIN, A DEVELOPMENTALLY REGULATED VERTEBRATE BETA-GALACTOSIDE BINDING PROTEIN
ComponentsBOVINE GALECTIN-1
KeywordsLECTIN
Function / homology
Function and homology information


Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / lactose binding / laminin binding / apoptotic process / extracellular space / 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
N-acetyl-alpha-lactosamine / Galectin-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsLiao, D.-I. / Herzberg, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of S-lectin, a developmentally regulated vertebrate beta-galactoside-binding protein.
Authors: Liao, D.I. / Kapadia, G. / Ahmed, H. / Vasta, G.R. / Herzberg, O.
History
DepositionOct 20, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BOVINE GALECTIN-1
B: BOVINE GALECTIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3455
Polymers29,5432
Non-polymers8023
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BOVINE GALECTIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1903
Polymers14,7721
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: BOVINE GALECTIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1552
Polymers14,7721
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.300, 62.900, 70.100
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: (0.947, -0.321, -0.035), (-0.321, -0.947, 0.013), (-0.037, -0.002, -0.993)
Vector: 14.39, 84.86, 52.35)
DetailsTHE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE RELATED TO EACH OTHER BY A NON-CRYSTALLOGRAPHIC TWO-FOLD ROTATION PERPENDICULAR TO THE BETA-SHEETS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein BOVINE GALECTIN-1


Mass: 14771.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: SPLEEN / References: UniProt: P11116
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS ONE CARBOHYDRATE BINDING SITE PER MONOMER. THE S-LECTIN DIMER FORMS A 22-STRAND ANTI- ...THERE IS ONE CARBOHYDRATE BINDING SITE PER MONOMER. THE S-LECTIN DIMER FORMS A 22-STRAND ANTI-PARALLEL BETA-SANDWICH WITH THE N- AND C- TERMINI OF EACH MONOMER AT THE DIMER INTERFACE.
Has protein modificationY
Sequence detailsTHE AMINO ACID SEQUENCE OF BOVINE SPLEEN LECTIN HAS NOT YET BEEN DETERMINED. THE ELECTRON DENSITY ...THE AMINO ACID SEQUENCE OF BOVINE SPLEEN LECTIN HAS NOT YET BEEN DETERMINED. THE ELECTRON DENSITY MAP IS CONSISTENT WITH THE SEQUENCE OF BOVINE HEART S-LECTIN. THUS THE MODEL IS BASED ON THAT SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21 mMN-acetyllactosamine1drop
32 mMdithiothreitol1drop
454-58 %satammonium sulphate1reservoir
5100 mMTris acetate1reservoir
60.5-2 %(v/v)MPD1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 20694 / % possible obs: 98 % / Num. measured all: 84959 / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.167 / Rfactor obs: 0.167 / Highest resolution: 1.9 Å
Details: THERE ARE SIX CYSTEINE RESIDUES IN EACH MONOMER. THE THIOL GROUPS OF CYS 42 AND CYS 60 ARE REDUCED IN BOTH MONOMERS. THE THIOL GROUP OF CYS 2 IS DISORDERED IN MOLECULE 1 (THE WHOLE OF ...Details: THERE ARE SIX CYSTEINE RESIDUES IN EACH MONOMER. THE THIOL GROUPS OF CYS 42 AND CYS 60 ARE REDUCED IN BOTH MONOMERS. THE THIOL GROUP OF CYS 2 IS DISORDERED IN MOLECULE 1 (THE WHOLE OF RESIDUE 2 IS DISORDERED IN MOLECULE 2). THE THIOL GROUPS OF CYS 16, CYS 88 AND CYS 130 ARE OXIDIZED. CYS 16 A, CYS 88 A, AND CYS 16 B WERE MODELED WITH TWO OXYGEN ATOMS COVALENTLY BOUND TO THE SULFUR ATOM. CYS 130 A, CYS 88 B AND CYS 130 B WERE MODELLED WITH ONLY ONE OXYGEN ATOM ATTACHED.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 53 154 2231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 18460 / σ(F): 2 / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.9

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