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- PDB-5glz: Tl-gal with Glucose -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5glz
TitleTl-gal with Glucose
Componentsgalectin
KeywordsSUGAR BINDING PROTEIN / Carbohydrates / Tl-galectin / Anti-inflammation
Function / homology
Function and homology information


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
beta-D-glucopyranose / Galectin
Similarity search - Component
Biological speciesToxascaris leonina (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
C: galectin
D: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0178
Polymers129,2974
Non-polymers7214
Water12,556697
1
A: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5042
Polymers32,3241
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5042
Polymers32,3241
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5042
Polymers32,3241
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5042
Polymers32,3241
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.646, 78.619, 83.023
Angle α, β, γ (deg.)89.90, 110.68, 105.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
galectin /


Mass: 32324.168 Da / Num. of mol.: 4
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: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
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: 2→30 Å / Num. obs: 114308 / % possible obs: 96.4 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.224

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HL0

4hl0


Resolution: 2→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2767 5215 4.6 %
Rwork0.2393 98031 -
obs-103246 90.5 %
Solvent computationBsol: 59.8004 Å2
Displacement parametersBiso max: 95.45 Å2 / Biso mean: 27.1991 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1--8.805 Å2-4.599 Å2-0.886 Å2
2--7.094 Å2-1.731 Å2
3---1.711 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8904 0 48 697 9649
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5231.5
X-RAY DIFFRACTIONc_scbond_it2.1752
X-RAY DIFFRACTIONc_mcangle_it2.4682
X-RAY DIFFRACTIONc_scangle_it3.2642.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3glu.param

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