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

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Basic information

Entry
Database: PDB / ID: 5duu
TitleCrystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / galectin-4 / lectin / glycerol / 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
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: 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 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _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

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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)70,2648
Polymers69,8964
Non-polymers3684
Water5,513306
1
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
2
B: 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
3
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
4
D: 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)63.238, 64.533, 64.685
Angle α, β, γ (deg.)90.000, 90.880, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA15 - 15115 - 151
21GLYGLYBB15 - 15115 - 151
12ILEILEAA15 - 15015 - 150
22ILEILECC15 - 15015 - 150
13ILEILEAA15 - 15015 - 150
23ILEILEDD15 - 15015 - 150
14ILEILEBB15 - 15015 - 150
24ILEILECC15 - 15015 - 150
15ILEILEBB15 - 15015 - 150
25ILEILEDD15 - 15015 - 150
16ILEILECC15 - 15015 - 150
26ILEILEDD15 - 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 1.89 Å3/Da / Density % sol: 34.86 %
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: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→45.68 Å / Num. obs: 35098 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.039 / Net I/σ(I): 15.8 / Num. measured all: 159500 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.054.30.2795.21101825340.9430.14997.4
8.95-45.684.20.02734.517224120.9990.01696.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I8T

3i8t


Resolution: 2→45.68 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2014 / WRfactor Rwork: 0.1682 / FOM work R set: 0.8463 / SU B: 4.273 / SU ML: 0.122 / SU R Cruickshank DPI: 0.2174 / SU Rfree: 0.1714 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The authors state that the electron density currently modelled as water molecules A301, B301 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 A301, B301 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
Rfree0.2219 1732 4.9 %RANDOM
Rwork0.1839 ---
obs0.1858 33349 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.42 Å2 / Biso mean: 18.537 Å2 / Biso min: 6.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0.16 Å2
2--1.61 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 2→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 24 306 4753
Biso mean--20.37 24.16 -
Num. residues----552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194614
X-RAY DIFFRACTIONr_bond_other_d0.0060.024316
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9326245
X-RAY DIFFRACTIONr_angle_other_deg1.3539902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21523.991233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50715717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4931520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215304
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021192
X-RAY DIFFRACTIONr_mcbond_it1.11.7382215
X-RAY DIFFRACTIONr_mcbond_other1.0991.7382214
X-RAY DIFFRACTIONr_mcangle_it1.8452.5952765
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A81400.12
12B81400.12
21A80520.11
22C80520.11
31A81350.11
32D81350.11
41B79110.13
42C79110.13
51B81110.11
52D81110.11
61C81490.11
62D81490.11
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 138 -
Rwork0.201 2394 -
all-2532 -
obs--97.46 %

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