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- PDB-5gm0: Tl-gal with lactose -

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Basic information

Entry
Database: PDB / ID: 5gm0
TitleTl-gal with lactose
Componentsgalectin
KeywordsSUGAR BINDING PROTEIN / Carbohydrates / Toxascaris leonina / Galectin
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-lactose / Galectin
Similarity search - Component
Biological speciesToxascaris leonina (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHwang, 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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_validate_close_contact / struct_asym / struct_conn / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: galectin
B: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6755
Polymers64,6482
Non-polymers1,0273
Water8,773487
1
A: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6662
Polymers32,3241
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint6 kcal/mol
Surface area13700 Å2
MethodPISA
2
B: galectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0093
Polymers32,3241
Non-polymers6852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint12 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.621, 84.392, 78.406
Angle α, β, γ (deg.)90.00, 109.24, 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: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: polyethylene glycol 4000, 0.1M Na HEPES pH 7.5, 0.1M ammonium sulfate

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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: 1.7→30 Å / Num. obs: 81697 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.7
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HL0

4hl0


Resolution: 1.7→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2724 3869 4.7 %
Rwork0.2418 72930 -
obs-76799 93.8 %
Solvent computationBsol: 64.5014 Å2
Displacement parametersBiso max: 80.23 Å2 / Biso mean: 26.6831 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1--4.625 Å20 Å2-4.66 Å2
2---1.746 Å20 Å2
3---6.371 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 69 487 5008
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4261.5
X-RAY DIFFRACTIONc_scbond_it2.1592
X-RAY DIFFRACTIONc_mcangle_it2.3082
X-RAY DIFFRACTIONc_scangle_it3.322.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2lat.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4carbohydrate.param

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