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- PDB-7als: Alpha and beta Lactose isomer structure of Galectin 8, N-terminal... -

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Basic information

Entry
Database: PDB / ID: 7als
TitleAlpha and beta Lactose isomer structure of Galectin 8, N-terminal domain
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / lactose / galectin
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / plasma cell differentiation / T cell costimulation / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane ...lymphatic endothelial cell migration / xenophagy / plasma cell differentiation / T cell costimulation / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / 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
beta-lactose / alpha-lactose / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHakansson, M. / Walse, B. / Diehl, C. / Kovacic, R.
CitationJournal: To Be Published
Title: Alpha and beta Lactose isomer structure of Galectin 8, N-terminal domain
Authors: Hassan, M. / Hakansson, M.
History
DepositionOct 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,5229
Polymers35,0462
Non-polymers1,4767
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-5 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.560, 62.540, 84.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 17523.096 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O00214
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 24% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→62.5 Å / Num. obs: 60843 / % possible obs: 99.8 % / Redundancy: 9.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18.8
Reflection shellResolution: 1.35→1.37 Å / Num. unique obs: 3044 / CC1/2: 0.36

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GZD

5gzd


Resolution: 1.35→41.15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.867 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19876 3292 5.1 %RANDOM
Rwork0.14935 ---
obs0.15181 60843 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.228 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2--2.6 Å20 Å2
3----1.66 Å2
Refinement stepCycle: 1 / Resolution: 1.35→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 95 367 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132646
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172432
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.6953613
X-RAY DIFFRACTIONr_angle_other_deg1.5011.6195696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3735326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36522.606142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65715445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1721516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022885
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02544
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9742.1531235
X-RAY DIFFRACTIONr_mcbond_other2.9342.1491233
X-RAY DIFFRACTIONr_mcangle_it3.1583.2371551
X-RAY DIFFRACTIONr_mcangle_other3.1583.2391552
X-RAY DIFFRACTIONr_scbond_it3.7482.5431411
X-RAY DIFFRACTIONr_scbond_other3.7442.5431411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4433.6792052
X-RAY DIFFRACTIONr_long_range_B_refined4.51727.012771
X-RAY DIFFRACTIONr_long_range_B_other4.44826.3362697
X-RAY DIFFRACTIONr_rigid_bond_restr4.50635078
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 246 -
Rwork0.308 4346 -
obs--97.41 %

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