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- PDB-8cm8: Galectin-8 N-terminal carbohydrate recognition domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 8cm8
TitleGalectin-8 N-terminal carbohydrate recognition domain in complex with 4-(bromophenyl)phthalazinone D-galactal ligand
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / Galectin / phthalazinone / inhibitor
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / extracellular space / membrane / cytoplasm / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsVan Klaveren, S. / Hakansson, M. / Diehl, C. / Nilsson, N.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581European Union
CitationJournal: To Be Published
Title: Halogenated Galactal-Phenylphthalazinone Hybrids as Highly Selective Galectin-8N Ligands
Authors: Van Klaveren, S. / Nilsson, N.J.
History
DepositionFeb 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-8
B: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6625
Polymers71,7082
Non-polymers9543
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-13 kcal/mol
Surface area14030 Å2
Unit cell
Length a, b, c (Å)54.710, 62.280, 84.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 35854.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Chemical ChemComp-V19 / 4-(4-bromophenyl)-2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]phthalazin-1-one


Mass: 459.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19BrN2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 8
Details: A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, ...Details: A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, was used to soak the compound by transferring crystals in three steps to soaking drops. These were 2 uL drops with a soaking solution of 20% ethylene glycol, 25% PEG 2000 MME, 10 mM Tris pH 8, 1 mM TCEP, 50 mM NaCl, and 2 mM compound 10. The incubation times in the first two drops were about 10 min and in the third drop about 24 h. Then the crystals were transferred to a cryo solution with the same constituents and flash-frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Sep 18, 2021
Details: Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.22→50.19 Å / Num. obs: 82202 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Χ2: 0.99 / Net I/σ(I): 13.5
Reflection shellResolution: 1.22→1.252 Å / Redundancy: 9 % / Rmerge(I) obs: 0.05 / Num. unique obs: 6317 / Rpim(I) all: 0.022 / Rrim(I) all: 0.054 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia20.3.6.3data reduction
Aimless0.7.7data scaling
PHASER2.7.14phasing
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→50.186 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.242 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.21391 4420 5.1 %Random
Rwork0.16897 82202 --
all0.172 ---
obs0.17119 82202 99.875 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.302 Å2
Baniso -1Baniso -2Baniso -3
1-0.142 Å20 Å2-0 Å2
2--0.361 Å20 Å2
3----0.503 Å2
Refinement stepCycle: LAST / Resolution: 1.22→50.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 59 289 2700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122586
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162470
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.6863520
X-RAY DIFFRACTIONr_angle_other_deg0.651.5995696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.644518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7910443
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.30810119
X-RAY DIFFRACTIONr_chiral_restr0.1050.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined0.2120.2363
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22167
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21207
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21347
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2178
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1410.28
X-RAY DIFFRACTIONr_nbd_other0.2040.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.221
X-RAY DIFFRACTIONr_mcbond_it1.9232.0791228
X-RAY DIFFRACTIONr_mcbond_other1.9182.0761227
X-RAY DIFFRACTIONr_mcangle_it2.2623.7321545
X-RAY DIFFRACTIONr_mcangle_other2.2613.7331545
X-RAY DIFFRACTIONr_scbond_it2.3492.4571358
X-RAY DIFFRACTIONr_scbond_other2.3492.4571358
X-RAY DIFFRACTIONr_scangle_it2.9384.3651968
X-RAY DIFFRACTIONr_scangle_other2.9374.3651969
X-RAY DIFFRACTIONr_lrange_it3.65426.0392812
X-RAY DIFFRACTIONr_lrange_other3.44923.7092745
X-RAY DIFFRACTIONr_rigid_bond_restr5.65335056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.2520.3923480.3875961X-RAY DIFFRACTION99.92
1.252-1.2860.3312950.3195889X-RAY DIFFRACTION99.9838
1.286-1.3230.3933440.3665635X-RAY DIFFRACTION99.8497
1.323-1.3640.2852910.2545597X-RAY DIFFRACTION99.983
1.364-1.4090.2712750.2255373X-RAY DIFFRACTION100
1.409-1.4580.2372710.1835219X-RAY DIFFRACTION99.9818
1.458-1.5130.2132570.1665053X-RAY DIFFRACTION100
1.513-1.5750.2212600.154854X-RAY DIFFRACTION99.9609
1.575-1.6450.1812390.1284654X-RAY DIFFRACTION100
1.645-1.7250.1922480.1244470X-RAY DIFFRACTION100
1.725-1.8180.1942260.1314227X-RAY DIFFRACTION100
1.818-1.9280.2312220.1643973X-RAY DIFFRACTION98.7524
1.928-2.0610.2182080.1463777X-RAY DIFFRACTION99.7747
2.061-2.2260.1822080.1413529X-RAY DIFFRACTION99.8397
2.226-2.4380.1991750.1553252X-RAY DIFFRACTION99.5353
2.438-2.7250.2261550.1662982X-RAY DIFFRACTION100
2.725-3.1450.2011420.1692644X-RAY DIFFRACTION99.9641
3.145-3.8480.1821010.1632275X-RAY DIFFRACTION99.9159
3.848-5.4260.187980.1571784X-RAY DIFFRACTION99.9469
5.426-50.1860.236570.2021054X-RAY DIFFRACTION99.9101

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