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- PDB-6z6y: Galectin-8 N-terminal domain in complex with a sulfatide mimickin... -

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Basic information

Entry
Database: PDB / ID: 6z6y
TitleGalectin-8 N-terminal domain in complex with a sulfatide mimicking a sphingolipid
ComponentsGalectin-8
KeywordsCELL ADHESION / Galectin-8 / Sphingolipid
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
ACETATE ION / Chem-L4L / TRIETHYLENE GLYCOL / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsRomero, A. / Medrano, F.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-77835-R Spain
CitationJournal: Iscience / Year: 2021
Title: Probing sulfatide-tissue lectin recognition with functionalized glycodendrimersomes.
Authors: Murphy, P.V. / Romero, A. / Xiao, Q. / Ludwig, A.K. / Jogula, S. / Shilova, N.V. / Singh, T. / Gabba, A. / Javed, B. / Zhang, D. / Medrano, F.J. / Kaltner, H. / Kopitz, J. / Bovin, N.V. / ...Authors: Murphy, P.V. / Romero, A. / Xiao, Q. / Ludwig, A.K. / Jogula, S. / Shilova, N.V. / Singh, T. / Gabba, A. / Javed, B. / Zhang, D. / Medrano, F.J. / Kaltner, H. / Kopitz, J. / Bovin, N.V. / Wu, A.M. / Klein, M.L. / Percec, V. / Gabius, H.J.
History
DepositionMay 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / cell / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[1][3] / _cell.angle_beta ..._atom_sites.fract_transf_matrix[1][3] / _cell.angle_beta / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _reflns.B_iso_Wilson_estimate / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Description: Ligand geometry / Details: We realized a problem with ligand geometry. / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,5289
Polymers17,6241
Non-polymers9048
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint3 kcal/mol
Surface area8430 Å2
Unit cell
Length a, b, c (Å)110.640, 40.066, 40.701
Angle α, β, γ (deg.)90.000, 99.803, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

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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: 17624.201 Da / Num. of mol.: 1
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-L4L / [(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S})-2-acetamido-3-oxidanylidene-pent-4-enoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate


Mass: 399.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21NO11S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1 M Na-HEPES, pH 7.6, 10% PEG 4000 and 20% Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 39289 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 20.36 Å2 / CC1/2: 1 / Net I/σ(I): 21.2
Reflection shellResolution: 1.34→1.42 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6233 / CC1/2: 0.823 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GZE

5gze


Resolution: 1.34→37.61 Å / SU ML: 0.1706 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1938 1998 5.09 %
Rwork0.1627 37233 -
obs0.1643 39231 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.86 Å2
Refinement stepCycle: LAST / Resolution: 1.34→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 60 122 1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881341
X-RAY DIFFRACTIONf_angle_d1.33511813
X-RAY DIFFRACTIONf_chiral_restr0.0838201
X-RAY DIFFRACTIONf_plane_restr0.0108236
X-RAY DIFFRACTIONf_dihedral_angle_d8.1411179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.43361370.46082537X-RAY DIFFRACTION95.98
1.38-1.410.32921420.32692633X-RAY DIFFRACTION99.75
1.41-1.460.28111400.25562647X-RAY DIFFRACTION99.79
1.46-1.50.29161450.21692680X-RAY DIFFRACTION99.89
1.5-1.560.21691410.19332631X-RAY DIFFRACTION99.64
1.56-1.620.23851420.17952652X-RAY DIFFRACTION99.71
1.62-1.690.2161440.15072675X-RAY DIFFRACTION99.89
1.69-1.780.18241440.14122660X-RAY DIFFRACTION99.89
1.78-1.890.17111420.13752655X-RAY DIFFRACTION100
1.89-2.040.18421420.14812678X-RAY DIFFRACTION99.75
2.04-2.240.18591430.14292658X-RAY DIFFRACTION99.86
2.24-2.570.17741440.15562690X-RAY DIFFRACTION99.86
2.57-3.240.19911440.16352670X-RAY DIFFRACTION99.61
3.24-37.610.17841480.15512767X-RAY DIFFRACTION99.59

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