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- PDB-4ym3: Crystal structure of the human galectin-4 C-terminal carbohydrate... -

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Basic information

Entry
Database: PDB / ID: 4ym3
TitleCrystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lactose
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / galectin / lectin / beta sandwich / carbohydrate recognition / lactose / carbohydrate binding protein
Function / homology
Function and homology information


antibacterial peptide biosynthetic process / galactoside binding / : / carbohydrate binding / 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
beta-lactose / Galectin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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_oper_list / 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.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _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 / 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)69,2188
Polymers67,8494
Non-polymers1,3694
Water5,927329
1
A: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3052
Polymers16,9621
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3052
Polymers16,9621
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3052
Polymers16,9621
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3052
Polymers16,9621
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.533, 130.185, 45.465
Angle α, β, γ (deg.)90.000, 96.910, 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
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
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


Mass: 18.015 Da / Num. of mol.: 329 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2 M Ammonium sulfate, 0.1 M HEPES pH 7.0, 4 % v/v PEG 400
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9713 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9713 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.446
11L, -K, H20.554
ReflectionResolution: 1.889→65.092 Å / Num. all: 41495 / Num. obs: 41495 / % possible obs: 98.9 % / Redundancy: 12.1 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.202 / Rsym value: 0.195 / Net I/av σ(I): 2.164 / Net I/σ(I): 15.8 / Num. measured all: 500962
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.87-1.987.10.5151.13326847170.2010.5154.891.5
1.98-2.18.30.4311.44928159190.1570.4316.3100
2.1-2.249.60.361.85369355760.1210.368100
2.24-2.4210.50.3271.55481952190.1060.3279100
2.42-2.6512.50.2752.25956547610.0810.27511100
2.65-2.96150.2282.46464743130.0610.22816.9100
2.96-3.42170.192.76515438310.0470.1927.5100
3.42-4.1916.90.1693.15512832540.0420.16935.7100
4.19-5.9316.90.1563.24218425030.0390.15639.4100
5.93-45.20216.60.1443.52322314020.0370.14442.399.8

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OJB

3ojb


Resolution: 1.89→45.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.1985 / WRfactor Rwork: 0.1719 / FOM work R set: 0.8342 / SU B: 2.828 / SU ML: 0.09 / SU R Cruickshank DPI: 0.0333 / SU Rfree: 0.0279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 2127 5.1 %RANDOM
Rwork0.1674 ---
obs0.1688 39334 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.57 Å2 / Biso mean: 20.778 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å2-0 Å23.34 Å2
2--9.01 Å20 Å2
3----7.18 Å2
Refinement stepCycle: final / Resolution: 1.89→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 92 329 4778
Biso mean--26.87 28.75 -
Num. residues----557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194580
X-RAY DIFFRACTIONr_bond_other_d0.0020.024325
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9696214
X-RAY DIFFRACTIONr_angle_other_deg0.84939940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.04222.692208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1791536
X-RAY DIFFRACTIONr_chiral_restr0.0720.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
X-RAY DIFFRACTIONr_mcbond_it0.7782.0362228
X-RAY DIFFRACTIONr_mcbond_other0.7782.0352227
X-RAY DIFFRACTIONr_mcangle_it1.3793.0492779
LS refinement shellResolution: 1.889→1.938 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 129 -
Rwork0.239 2458 -
all-2587 -
obs--84.68 %

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