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

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Basic information

Entry
Database: PDB / ID: 5dux
TitleCrystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with 2'-fucosyllactose
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / galectin-4 / H-antigen / 2'-fucosyllactose / 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
2'-fucosyllactose / FORMIC ACID / Galectin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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_assembly_gen / pdbx_struct_oper_list / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Galectin-4
D: Galectin-4
A: Galectin-4
C: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1039
Polymers69,8964
Non-polymers1,2075
Water7,909439
1
B: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9622
Polymers17,4741
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0083
Polymers17,4741
Non-polymers5342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5662
Polymers17,4741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5662
Polymers17,4741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.152, 64.469, 64.653
Angle α, β, γ (deg.)90.000, 90.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12B
22A
13B
23C
14D
24A
15D
25C
16A
26C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEBA15 - 15015 - 150
21ILEILEDB15 - 15015 - 150
12GLYGLYBA15 - 15215 - 152
22GLYGLYAC15 - 15215 - 152
13ILEILEBA15 - 15015 - 150
23ILEILECD15 - 15015 - 150
14ILEILEDB15 - 15015 - 150
24ILEILEAC15 - 15015 - 150
15GLYGLYDB15 - 15115 - 151
25GLYGLYCD15 - 15115 - 151
16ILEILEAC15 - 15015 - 150
26ILEILECD15 - 15015 - 150

NCS ensembles :
ID
1
2
3
4
5
6

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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 alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 2'-fucosyllactose


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2'-fucosyllactose
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 1.88 Å3/Da / Density % sol: 34.67 %
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: 1.85→45.65 Å / Num. obs: 44028 / % possible obs: 99.1 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.024 / Net I/σ(I): 22.9 / Num. measured all: 177950
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.85-1.893.40.1258.9899726260.9810.07996.2
9.06-45.653.50.03233.813403780.9980.02194.4

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I8T

3i8t


Resolution: 1.85→45.65 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2058 / WRfactor Rwork: 0.1675 / FOM work R set: 0.8674 / SU B: 2.93 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1482 / SU Rfree: 0.1326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The authors state that the electron density currently modelled as water molecules A302, B303 and D301, which are coordinated by residues ASP72, GLY70 and PHE68 shows potential for occupation ...Details: The authors state that the electron density currently modelled as water molecules A302, B303 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
Rfree0.2046 2156 4.9 %RANDOM
Rwork0.1662 ---
obs0.1681 41855 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.16 Å2 / Biso mean: 18.033 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å2-0.01 Å2
2--1.59 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.85→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 81 439 4928
Biso mean--27.25 26.49 -
Num. residues----550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194637
X-RAY DIFFRACTIONr_bond_other_d0.0020.024312
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.9486278
X-RAY DIFFRACTIONr_angle_other_deg0.67539892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3485548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09323.886229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14115706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4341520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215248
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021180
X-RAY DIFFRACTIONr_mcbond_it1.7571.5462198
X-RAY DIFFRACTIONr_mcbond_other1.7521.5452197
X-RAY DIFFRACTIONr_mcangle_it2.5882.3062741
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B79590.13
12D79590.13
21B80700.12
22A80700.12
31B77520.15
32C77520.15
41D80350.12
42A80350.12
51D80910.12
52C80910.12
61A78820.13
62C78820.13
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 133 -
Rwork0.201 3018 -
all-3151 -
obs--96.48 %

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