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- PDB-5duw: Crystal structure of the human galectin-4 N-terminal carbohydrate... -

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Basic information

Entry
Database: PDB / ID: 5duw
TitleCrystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with lactose-3'-sulfate
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / galectin-4 / lectin / sulfate / sugar-binding protein
Function / homology
Function and homology information


antibacterial peptide biosynthetic process / galactoside binding / carbohydrate binding / collagen-containing extracellular matrix / cell adhesion / extracellular space / plasma membrane / 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
lactose-3'-sulfate / Galectin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBum-Erdene, K. / Blanchard, H.
Funding support Australia, 1items
OrganizationGrant numberCountry
Cancer Council Queensland1043716 Australia
CitationJournal: Sci Rep / Year: 2016
Title: Structural characterisation of human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol, lactose, 3'-sulfo-lactose, and 2'-fucosyllactose.
Authors: Bum-Erdene, K. / Leffler, H. / Nilsson, U.J. / Blanchard, H.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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_oper_list / pdbx_validate_close_contact / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.type / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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-4
B: Galectin-4
C: Galectin-4
D: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5858
Polymers69,8964
Non-polymers1,6894
Water10,052558
1
A: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8962
Polymers17,4741
Non-polymers4221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8962
Polymers17,4741
Non-polymers4221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8962
Polymers17,4741
Non-polymers4221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8962
Polymers17,4741
Non-polymers4221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.180, 64.050, 64.650
Angle α, β, γ (deg.)90.00, 91.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Galectin-4 / / Gal-4 / Antigen NY-CO-27 / L-36 lactose-binding protein / L36LBP / Lactose-binding lectin 4


Mass: 17473.912 Da / Num. of mol.: 4
Fragment: N-terminal carbohydrate recognition domain (UNP residues 1-155)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS4 / Production host: Escherichia coli (E. coli) / References: UniProt: P56470
#2: Polysaccharide
3-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / lactose-3'-sulfate


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 422.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactose-3'-sulfate
DescriptorTypeProgram
DGalp[3S]b1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5_3*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp3SO3]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 1.87 Å3/Da / Density % sol: 34.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 3.5 M sodium formate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→64.64 Å / Num. obs: 56576 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Aimless0.3.6data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I8T

3i8t


Resolution: 1.7→64.64 Å / SU B: 2.102 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.097
Details: The authors state that the electron density currently modelled as water molecules A304, B302, C301 and D301, which are coordinated by residues ASP72, GLY70 and PHE68 shows potential for ...Details: The authors state that the electron density currently modelled as water molecules A304, B302, C301 and D301, which are coordinated by residues ASP72, GLY70 and PHE68 shows potential for occupation by NA+ ions, which is present in the crystallisation conditions.
RfactorNum. reflection% reflectionSelection details
Rfree0.181 2795 4.9 %RANDOM
Rwork0.149 ---
obs0.151 53758 99.5 %-
Displacement parametersBiso mean: 16.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-0.22 Å2
2--1.97 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→64.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4416 0 108 558 5082
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.235 250 -
Rwork0.221 --
obs-4132 98.8 %

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