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- PDB-5jpg: Rat Galectin 5 with lactose -

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Basic information

Entry
Database: PDB / ID: 5jpg
TitleRat Galectin 5 with lactose
ComponentsGalectin-5
KeywordsSUGAR BINDING PROTEIN / lectin / carbohydrate recognition / jellyroll topology
Function / homology
Function and homology information


lactose binding / galactoside binding / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of T cell apoptotic process / negative regulation of type II interferon production / carbohydrate binding / positive regulation of gene expression / nucleus / cytosol
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
alpha-lactose / Galectin-5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRomero, A. / Ruiz, F.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science and InnovationBFU2011-24615 Spain
CitationJournal: Biomolecules / Year: 2021
Title: Structural Characterization of Rat Galectin-5, an N-Tailed Monomeric Proto-Type-like Galectin.
Authors: Ruiz, F.M. / Medrano, F.J. / Ludwig, A.K. / Kaltner, H. / Shilova, N.V. / Bovin, N.V. / Gabius, H.J. / Romero, A.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.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.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 2, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jan 10, 2024Group: 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-5
B: Galectin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1325
Polymers32,4252
Non-polymers7083
Water4,954275
1
A: Galectin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5783
Polymers16,2121
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5552
Polymers16,2121
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.024, 65.763, 112.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Galectin-5 / / Gal-5 / RL-18


Mass: 16212.335 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lgals5 / Production host: Escherichia coli (E. coli) / References: UniProt: P47967
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-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: 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% PEG 8000, 100 mM Tris pH 7.0, 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→39.024 Å / Num. obs: 23584 / % possible obs: 99.78 % / Redundancy: 2 % / Biso Wilson estimate: 15.69 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.74 / % possible all: 99.74

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NV1

3nv1


Resolution: 1.9→39.024 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.05
RfactorNum. reflection% reflection
Rfree0.2275 1190 5.05 %
Rwork0.178 --
obs0.1805 23576 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 47 275 2515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132332
X-RAY DIFFRACTIONf_angle_d0.9223176
X-RAY DIFFRACTIONf_dihedral_angle_d15.8411364
X-RAY DIFFRACTIONf_chiral_restr0.062360
X-RAY DIFFRACTIONf_plane_restr0.006413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.98650.29691510.21942741X-RAY DIFFRACTION100
1.9865-2.09130.25591420.18432751X-RAY DIFFRACTION100
2.0913-2.22230.21921510.18742749X-RAY DIFFRACTION100
2.2223-2.39380.25521350.18272789X-RAY DIFFRACTION100
2.3938-2.63470.24541440.18492791X-RAY DIFFRACTION100
2.6347-3.01580.26341390.19052800X-RAY DIFFRACTION100
3.0158-3.79910.20531550.15922826X-RAY DIFFRACTION100
3.7991-39.03220.19031730.16542939X-RAY DIFFRACTION99

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