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- PDB-5glv: Tl-gal -

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Basic information

Entry
Database: PDB / ID: 5glv
TitleTl-gal
Componentsgalectin
KeywordsSUGAR BINDING PROTEIN / Crystal Structures / Carbohydrates / Toxascaris leonina / Galectin
Function / homology
Function and homology information


galactoside binding / carbohydrate binding
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
Biological speciesToxascaris leonina (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsJang, S.B. / Hwang, E.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea2015R1D1A1A01059594 Korea, Republic Of
Citation
Journal: J. Biol. Chem. / Year: 2016
Title: Structural Basis for Carbohydrate Recognition and Anti-inflammatory Modulation by Gastrointestinal Nematode Parasite Toxascaris leonina Galectin
Authors: Hwang, E.Y. / Jeong, M.S. / Park, S.K. / Ha, S.C. / Yu, H.S. / Jang, S.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of full-length Toxascaris leonina galectin with two carbohydrate-recognition domains
Authors: Jeong, M.S. / Hwang, H.G. / Yu, H.S. / Jang, S.B.
History
DepositionJul 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
B: galectin


Theoretical massNumber of molelcules
Total (without water)64,6482
Polymers64,6482
Non-polymers00
Water9,350519
1
A: galectin


Theoretical massNumber of molelcules
Total (without water)32,3241
Polymers32,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: galectin


Theoretical massNumber of molelcules
Total (without water)32,3241
Polymers32,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.419, 83.998, 78.356
Angle α, β, γ (deg.)90.00, 109.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein galectin


Mass: 32324.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxascaris leonina (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L1QJZ7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% polyethylene glycol 8000, 100mM Na/K phosphate (pH 6.2), 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: MAC Science DIP-320 / Detector: IMAGE PLATE / Date: Jun 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 67664 / % possible obs: 97.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.381

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementResolution: 1.8→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.258 3252 4.8 %
Rwork0.2232 --
obs-64125 93.9 %
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 0 519 4971

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