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- PDB-4hl0: Crystal structure of full-length Toxascaris leonina galectin -

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Basic information

Entry
Database: PDB / ID: 4hl0
TitleCrystal structure of full-length Toxascaris leonina galectin
Componentsgalectin
KeywordsSUGAR BINDING PROTEIN / Carbohydrate Recognition Domain / Galectin / a regulatory molecule / the host immune system
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJeong, M.S.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 2010
Title: X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose.
Authors: Yoshida, H. / Teraoka, M. / Nishi, N. / Nakakita, S. / Nakamura, T. / Hirashima, M. / Kamitori, S.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Mar 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

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Assembly

Deposited unit
A: galectin
B: galectin


Theoretical massNumber of molelcules
Total (without water)62,9912
Polymers62,9912
Non-polymers00
Water7,981443
1
A: galectin


Theoretical massNumber of molelcules
Total (without water)31,4951
Polymers31,4951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: galectin


Theoretical massNumber of molelcules
Total (without water)31,4951
Polymers31,4951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.573, 82.827, 122.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein galectin


Mass: 31495.289 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: F1KZZ8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% 2-propanol, 0.1M MES buffer pH 6.0, 0.2M Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2012
RadiationMonochromator: Cu FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 97056 / Num. obs: 54560 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 25.7 / Num. unique all: 97056 / Rsym value: 0.102 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.293 2595 RANDOM
Rwork0.254 --
all0.293 51779 -
obs0.254 49184 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 0 443 4895
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2→2.03 Å
RfactorNum. reflection% reflection
Rfree0.293 2592 -
Rwork0.254 --
obs-49184 99.3 %

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