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- PDB-6wab: Crystal structure of human galectin-4 C-terminal carbohydrate rec... -

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Basic information

Entry
Database: PDB / ID: 6wab
TitleCrystal structure of human galectin-4 C-terminal carbohydrate recognition domain in complex with galactose derivative
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / GALECTIN / LECTIN / BETA SANDWICH / CARBOHYDRATE RECOGNITION / 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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-U61 / Galectin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsGo, R.M. / Kishor, C. / Blanchard, H.
CitationJournal: To Be Published
Title: Crystal structure of human galectin-4 C-terminal carbohydrate recognition domain in complex with galactose derivative
Authors: Go, R.M. / Kishor, C. / Blanchard, H.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)62,8798
Polymers61,7624
Non-polymers1,1174
Water1,67593
1
A: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0914
Polymers15,4411
Non-polymers6513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9072
Polymers15,4411
Non-polymers4661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galectin-4


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galectin-4


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.698, 128.558, 45.891
Angle α, β, γ (deg.)90.000, 101.219, 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: 15440.567 Da / Num. of mol.: 4 / Fragment: C-terminal carbohydrate recognition domain
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-U61 / 2,6-anhydro-1,4-dideoxy-1-[4-(4-fluorophenyl)-1H-1,2,3-triazol-1-yl]-4-(4-phenyl-1H-1,2,3-triazol-1-yl)-D-glycero-L-manno-heptitol


Mass: 466.465 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23FN6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6 M ammonium sulfate, 4% (v/v) polyethylene glycol (PEG) 400, 0.1 M HEPES pH 7.0
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.28→45.01 Å / Num. obs: 23306 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.992 / Net I/σ(I): 6.8
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 2251 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YM2

4ym2


Resolution: 2.28→36.795 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.744 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.49 / ESU R Free: 0.281
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2662 1214 5.219 %
Rwork0.1967 --
all0.2 --
obs-23261 98.343 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.074 Å2
Baniso -1Baniso -2Baniso -3
1-0.023 Å20 Å2-0.003 Å2
2---0.025 Å20 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 2.28→36.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 80 93 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134552
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174182
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6776172
X-RAY DIFFRACTIONr_angle_other_deg1.2081.5929678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4665552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.32820.694245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93615703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.851537
X-RAY DIFFRACTIONr_chiral_restr0.0650.2574
X-RAY DIFFRACTIONr_chiral_restr_other1.5270.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021061
X-RAY DIFFRACTIONr_nbd_refined0.1980.2702
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23875
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22076
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.22275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2165
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.231
X-RAY DIFFRACTIONr_nbd_other0.2050.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.215
X-RAY DIFFRACTIONr_mcbond_it3.0973.7222208
X-RAY DIFFRACTIONr_mcbond_other3.0973.7222207
X-RAY DIFFRACTIONr_mcangle_it4.4455.5692754
X-RAY DIFFRACTIONr_mcangle_other4.4455.572755
X-RAY DIFFRACTIONr_scbond_it3.3453.9812344
X-RAY DIFFRACTIONr_scbond_other3.3453.9822344
X-RAY DIFFRACTIONr_scangle_it4.9035.8463416
X-RAY DIFFRACTIONr_scangle_other4.9025.8463416
X-RAY DIFFRACTIONr_lrange_it6.97742.1034644
X-RAY DIFFRACTIONr_lrange_other6.97942.1064640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.3390.313930.2111593X-RAY DIFFRACTION98.2517
2.339-2.4030.306840.2391613X-RAY DIFFRACTION98.2629
2.403-2.4730.322710.2191530X-RAY DIFFRACTION98.5231
2.473-2.5490.359830.2291520X-RAY DIFFRACTION98.0428
2.549-2.6320.297990.1991424X-RAY DIFFRACTION99.3477
2.632-2.7240.299870.2081399X-RAY DIFFRACTION97.9565
2.724-2.8270.242810.1951359X-RAY DIFFRACTION99.1053
2.827-2.9420.297680.191307X-RAY DIFFRACTION98.7078
2.942-3.0730.264550.1851288X-RAY DIFFRACTION98.3883
3.073-3.2220.285670.1821186X-RAY DIFFRACTION99.1297
3.222-3.3960.228470.1811150X-RAY DIFFRACTION98.681
3.396-3.6020.292800.1871054X-RAY DIFFRACTION97.6744
3.602-3.8490.204420.1921012X-RAY DIFFRACTION96.5201
3.849-4.1570.245570.184968X-RAY DIFFRACTION98.7476
4.157-4.5510.198440.17869X-RAY DIFFRACTION99.3471
4.551-5.0860.286510.182785X-RAY DIFFRACTION98.7013
5.086-5.8660.282310.205706X-RAY DIFFRACTION98.5294
5.866-7.170.261400.21573X-RAY DIFFRACTION97.9233
7.17-10.0770.216190.213460X-RAY DIFFRACTION97.1602

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