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- PDB-5jp5: Crystal structure of rat Galectin 5 -

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Basic information

Entry
Database: PDB / ID: 5jp5
TitleCrystal structure of rat Galectin 5
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
DI(HYDROXYETHYL)ETHER / Galectin-5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRuiz, F.M. / Romero, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
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 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._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 1.2Jan 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
C: Galectin-5
D: Galectin-5
E: Galectin-5
F: Galectin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,69810
Polymers97,2746
Non-polymers4244
Water15,295849
1
A: Galectin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3182
Polymers16,2121
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-5


Theoretical massNumber of molelcules
Total (without water)16,2121
Polymers16,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galectin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3182
Polymers16,2121
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galectin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3182
Polymers16,2121
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Galectin-5


Theoretical massNumber of molelcules
Total (without water)16,2121
Polymers16,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Galectin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3182
Polymers16,2121
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.088, 68.124, 95.346
Angle α, β, γ (deg.)90.00, 91.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16212.335 Da / Num. of mol.: 6
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: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / 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: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.7→33.03 Å / Num. obs: 92950 / % possible obs: 99.75 % / Redundancy: 4.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.01
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / % possible all: 99.21

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Processing

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

3nv1


Resolution: 1.7→33.027 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.14
RfactorNum. reflection% reflection
Rfree0.2144 4661 5.02 %
Rwork0.1741 --
obs0.1761 92868 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→33.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 28 849 7435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066892
X-RAY DIFFRACTIONf_angle_d0.8019409
X-RAY DIFFRACTIONf_dihedral_angle_d13.9354166
X-RAY DIFFRACTIONf_chiral_restr0.0631037
X-RAY DIFFRACTIONf_plane_restr0.0061248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.29811440.24942877X-RAY DIFFRACTION100
1.7193-1.73950.28551700.23642966X-RAY DIFFRACTION100
1.7395-1.76080.26311440.22372942X-RAY DIFFRACTION100
1.7608-1.7830.25311570.2172904X-RAY DIFFRACTION100
1.783-1.80650.24811450.20322936X-RAY DIFFRACTION100
1.8065-1.83120.25331470.20562952X-RAY DIFFRACTION100
1.8312-1.85740.25311540.19552916X-RAY DIFFRACTION100
1.8574-1.88510.22841770.18332931X-RAY DIFFRACTION100
1.8851-1.91460.23461530.18472902X-RAY DIFFRACTION100
1.9146-1.9460.23031630.19092966X-RAY DIFFRACTION100
1.946-1.97950.22361630.18632900X-RAY DIFFRACTION100
1.9795-2.01550.21081500.18522928X-RAY DIFFRACTION100
2.0155-2.05430.23591490.18272944X-RAY DIFFRACTION100
2.0543-2.09620.22531530.18092910X-RAY DIFFRACTION100
2.0962-2.14180.23591410.17662966X-RAY DIFFRACTION100
2.1418-2.19160.23031650.17852930X-RAY DIFFRACTION100
2.1916-2.24640.19981530.17492906X-RAY DIFFRACTION100
2.2464-2.30710.23471530.17012948X-RAY DIFFRACTION100
2.3071-2.3750.21381810.16862927X-RAY DIFFRACTION100
2.375-2.45160.21281430.16992961X-RAY DIFFRACTION100
2.4516-2.53920.21561540.16812919X-RAY DIFFRACTION100
2.5392-2.64080.25791580.17292962X-RAY DIFFRACTION100
2.6408-2.76090.18711770.1742908X-RAY DIFFRACTION100
2.7609-2.90640.21661570.17512953X-RAY DIFFRACTION100
2.9064-3.08840.20031550.16382970X-RAY DIFFRACTION100
3.0884-3.32670.21751620.1622932X-RAY DIFFRACTION100
3.3267-3.6610.20351390.15742993X-RAY DIFFRACTION100
3.661-4.18990.16781520.14832965X-RAY DIFFRACTION100
4.1899-5.27540.13851410.13983004X-RAY DIFFRACTION100
5.2754-33.03320.24691610.19332989X-RAY DIFFRACTION98

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