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- PDB-5vwg: Galectin-8 N terminal domain in complex with Methyl 3-O-[1-carbox... -

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Basic information

Entry
Database: PDB / ID: 5vwg
TitleGalectin-8 N terminal domain in complex with Methyl 3-O-[1-carboxyethyl]-beta-D-galactopyranoside
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding protein / galectin-8N terminal domain / galectin-8N in complex with designed ligand / Methyl 3-O-[1-carboxyehtyl]-b-D-galactopyranoside
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane / cytosol / cytoplasm
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
Chem-9QG / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBohari, M.H. / Yu, X. / Blanchard, H.
CitationJournal: To Be Published
Title: Galectin-8 N terminal domain in complex with Methyl 3-O-[1-carboxyethyl]-beta-D-galactopyranoside
Authors: Blanchard, H. / Yu, X. / Bohari, M.H.
History
DepositionMay 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 4, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7922
Polymers17,5261
Non-polymers2661
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.777, 50.145, 80.695
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: 17526.203 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-155) / Mutation: M56V
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: Sugar ChemComp-9QG / methyl 3-O-[(1R)-1-carboxyethyl]-beta-D-galactopyranoside / methyl 3-O-[(1R)-1-carboxyethyl]-beta-D-galactoside / methyl 3-O-[(1R)-1-carboxyethyl]-D-galactoside / methyl 3-O-[(1R)-1-carboxyethyl]-galactoside


Type: D-saccharide / Mass: 266.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H18O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→26.9 Å / Num. obs: 11077 / % possible obs: 98 % / Redundancy: 4.9 % / CC1/2: 0.981 / Rmerge(I) obs: 0.149 / Net I/σ(I): 5.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 873 / CC1/2: 0.546 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T7U

5t7u


Resolution: 2.1→26.9 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.63 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R: 0.236 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25084 569 5.1 %RANDOM
Rwork0.22009 ---
obs0.2217 10508 97.61 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.404 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 18 112 1305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191228
X-RAY DIFFRACTIONr_bond_other_d0.0010.021188
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9651664
X-RAY DIFFRACTIONr_angle_other_deg0.82932735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36523.68457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99715205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.531158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
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_it3.4792.291589
X-RAY DIFFRACTIONr_mcbond_other3.4812.286588
X-RAY DIFFRACTIONr_mcangle_it4.8053.418735
X-RAY DIFFRACTIONr_mcangle_other4.8063.423736
X-RAY DIFFRACTIONr_scbond_it5.4382.869639
X-RAY DIFFRACTIONr_scbond_other5.4322.869639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.94.06929
X-RAY DIFFRACTIONr_long_range_B_refined9.80719.381294
X-RAY DIFFRACTIONr_long_range_B_other9.80419.3871295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 38 -
Rwork0.331 733 -
obs--94.6 %

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