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- PDB-4ym1: Crystal structure of the human galectin-4 C-terminal carbohydrate... -

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Basic information

Entry
Database: PDB / ID: 4ym1
TitleCrystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with 2'-fucosyllactose
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / galectin / lectin / carbohydrate binding protein / H-antigen / carbohydrate recognition / beta sandwich
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 / Galectin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBum-Erdene, K. / Blanchard, H.
Funding support Australia, 1items
OrganizationGrant numberCountry
Cancer Council Queensland1043716 Australia
CitationJournal: Febs J. / Year: 2015
Title: Structural characterization of human galectin-4 C-terminal domain: elucidating the molecular basis for recognition of glycosphingolipids, sulfated saccharides and blood group antigens.
Authors: Bum-Erdene, K. / Leffler, H. / Nilsson, U.J. / Blanchard, H.
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
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
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

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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)69,1149
Polymers67,8494
Non-polymers1,2655
Water2,144119
1
A: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6434
Polymers16,9621
Non-polymers6813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4512
Polymers16,9621
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0582
Polymers16,9621
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-4


Theoretical massNumber of molelcules
Total (without water)16,9621
Polymers16,9621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.292, 129.962, 45.207
Angle α, β, γ (deg.)90.000, 96.960, 90.000
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: 16962.291 Da / Num. of mol.: 4 / Fragment: unp residues 171-323
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2 M Ammonium sulfate, 0.1 M HEPES, 4 % v/v PEG 400

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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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.447
11L, -K, H20.553
ReflectionResolution: 2→44.96 Å / Num. obs: 34862 / % possible obs: 99.7 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.052 / Net I/σ(I): 12.3 / Num. measured all: 172036 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Redundancy: 4 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.050.2746.31019525750.8660.15799.5
8.94-44.960.03324.516294040.9980.01999.1

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.3.6data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OJB

3ojb


Resolution: 2→44.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2286 / WRfactor Rwork: 0.1678 / FOM work R set: 0.8324 / SU B: 4.316 / SU ML: 0.124 / SU R Cruickshank DPI: 0.0388 / SU Rfree: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1718 4.9 %RANDOM
Rwork0.1626 ---
obs0.165 33112 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.32 Å2 / Biso mean: 32.147 Å2 / Biso min: 17.58 Å2
Baniso -1Baniso -2Baniso -3
1--9.29 Å2-0 Å20.41 Å2
2--9.76 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 81 119 4550
Biso mean--44.79 31.86 -
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194550
X-RAY DIFFRACTIONr_bond_other_d0.0020.024300
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9646164
X-RAY DIFFRACTIONr_angle_other_deg1.20239864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.43622.692208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0031536
X-RAY DIFFRACTIONr_chiral_restr0.1150.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021144
X-RAY DIFFRACTIONr_mcbond_it1.3463.1852220
X-RAY DIFFRACTIONr_mcbond_other1.3463.1852219
X-RAY DIFFRACTIONr_mcangle_it2.2134.7712768
LS refinement shellResolution: 1.997→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 146 -
Rwork0.191 2256 -
all-2402 -
obs--93.17 %

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