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

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Basic information

Entry
Database: PDB / ID: 5duv
TitleCrystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with lactose
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / galectin-4 / lectin / lactose / sugar-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 / ACETATE ION / Galectin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: 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_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
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)71,54314
Polymers69,8964
Non-polymers1,64810
Water6,846380
1
A: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8563
Polymers17,4741
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8563
Polymers17,4741
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9154
Polymers17,4741
Non-polymers4413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9154
Polymers17,4741
Non-polymers4413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.920, 64.750, 64.470
Angle α, β, γ (deg.)90.000, 91.260, 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: 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
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 34.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.2 M calcium acetate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→37.24 Å / Num. obs: 40168 / % possible obs: 98.1 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.044 / Net I/σ(I): 12.2 / Num. measured all: 161697 / Scaling rejects: 168
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
1.9-1.943.20.2674.1685421280.8980.17782.1
9.11-37.243.60.04318.414253920.9970.02598.7

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I8T

3i8t


Resolution: 1.9→37.24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1926 / WRfactor Rwork: 0.1506 / FOM work R set: 0.8706 / SU B: 3.264 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1577 / SU Rfree: 0.1396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 2016 5 %RANDOM
Rwork0.1552 ---
obs0.1574 38075 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.66 Å2 / Biso mean: 17.307 Å2 / Biso min: 5.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å20.1 Å2
2--0.74 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.9→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 104 380 4892
Biso mean--18.22 24.5 -
Num. residues----550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194732
X-RAY DIFFRACTIONr_bond_other_d00.024396
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9556435
X-RAY DIFFRACTIONr_angle_other_deg0.514310116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0235570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21623.95238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58715728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0551522
X-RAY DIFFRACTIONr_chiral_restr0.0640.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215390
X-RAY DIFFRACTIONr_gen_planes_other00.021212
X-RAY DIFFRACTIONr_mcbond_it1.741.5112225
X-RAY DIFFRACTIONr_mcbond_other1.7311.5092222
X-RAY DIFFRACTIONr_mcangle_it2.522.252779
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 131 -
Rwork0.207 2322 -
all-2453 -
obs--82.12 %

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