data_21032 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of 1,3-Fucosylated chitobiose ; _BMRB_accession_number 21032 _BMRB_flat_file_name bmr21032.str _Entry_type new _Submission_date 2013-01-21 _Accession_date 2013-01-24 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; GlcNAc-beta1,4-[Fuc-alpha1,3-]GlcNAc-beta-spacer; it is a trisaccharide with a O(CH2)5COOH spacer ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schubert Mario . . 2 Allain Frederic . . 3 Aeschbacher Thomas . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 78 "13C chemical shifts" 52 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-08-30 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 19748 'Solution structure of Lactodifucotetraose (LDFT) beta anomer' 21031 'Solution structure of Lewis a [Gal-beta1_3-(Fuc-alpha1_4-)GlcNAc-beta-Me]' 21033 'Solution structure of Lewis x (Gal-beta1,4-[Fuc-alpha1,3]-GlcNAc-beta) attached to a protein' 21034 'Solution structure of Lewisx (Gal-beta1,4-[Fuc-alpha1,3-]GlcNAc-beta-OMe)at 277 K' 21053 'Solution structure of fucosylated LacDiNAc (LDNF)' 21054 'Solution structure of the amphibian egg glycan Bv9 from Bombina variegata' stop_ _Original_release_date 2013-01-24 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; A Secondary Structural Element in a Wide Range of Fucosylated Glycoepitopes. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28654715 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Aeschbacher Thomas . . 2 Zierke Mirko . . 3 Smiesko Martin . . 4 Collot Mayeul . . 5 Mallet Jean-Maurice M. . 6 Ernst Beat . . 7 Allain 'Frederic H-T' H. . 8 Schubert Mario . . stop_ _Journal_abbreviation Chemistry _Journal_name_full 'Chemistry (Weinheim an der Bergstrasse, Germany)' _Journal_volume 23 _Journal_issue 48 _Journal_ISSN 1521-3765 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11598 _Page_last 11610 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'SUGAR (3-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'SUGAR (3-MER)' $SUGAR_(3-MER) stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SUGAR_(3-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class carbohydrate _Name_common SUGAR_(3-MER) _Molecular_mass 684.69 _Mol_thiol_state 'not present' loop_ _Biological_function 'core 1,3-fucosylation of N-glycans in invertebrates and plants' stop_ _Details 'The trisaccharide was chemically synthesized.' ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence ; XXXX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 6HH 2 2 NAG 3 3 NAG 4 4 FUC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NAG _Saveframe_category polymer_residue _Mol_type D-SACCHARIDE _Name_common N-ACETYL-D-GLUCOSAMINE _BMRB_code NAG _PDB_code NAG _Standard_residue_derivative . _Molecular_mass 221.208 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? N2 N2 N . 0 . ? O1 O1 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 0 . ? O6 O6 O . 0 . ? O7 O7 O . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H81 H81 H . 0 . ? H82 H82 H . 0 . ? H83 H83 H . 0 . ? HN2 HN2 H . 0 . ? HO1 HO1 H . 0 . ? HO3 HO3 H . 0 . ? HO4 HO4 H . 0 . ? HO6 HO6 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING C1 C2 ? ? SING C1 O1 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 N2 ? ? SING C2 H2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 O4 ? ? SING C4 H4 ? ? SING C5 C6 ? ? SING C5 O5 ? ? SING C5 H5 ? ? SING C6 O6 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING C7 C8 ? ? SING C7 N2 ? ? DOUB C7 O7 ? ? SING C8 H81 ? ? SING C8 H82 ? ? SING C8 H83 ? ? SING N2 HN2 ? ? SING O1 HO1 ? ? SING O3 HO3 ? ? SING O4 HO4 ? ? SING O6 HO6 ? ? stop_ save_ save_chem_comp_FUC _Saveframe_category polymer_residue _Mol_type SACCHARIDE _Name_common ALPHA-L-FUCOSE _BMRB_code FUC _PDB_code FUC _Standard_residue_derivative . _Molecular_mass 164.156 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H63 H63 H . 0 . ? HO1 HO1 H . 0 . ? HO2 HO2 H . 0 . ? HO3 HO3 H . 0 . ? HO4 HO4 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING C1 C2 ? ? SING C1 O1 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING C2 C3 ? ? SING C2 O2 ? ? SING C2 H2 ? ? SING C3 C4 ? ? SING C3 O3 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 O4 ? ? SING C4 H4 ? ? SING C5 C6 ? ? SING C5 O5 ? ? SING C5 H5 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING C6 H63 ? ? SING O1 HO1 ? ? SING O2 HO2 ? ? SING O3 HO3 ? ? SING O4 HO4 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $SUGAR_(3-MER) nematode 6239 Eukaryota Metazoa Caenorhabditis elegans stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $SUGAR_(3-MER) 'chemically synthesized' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SUGAR_(3-MER) 2.8 mM 'natural abundance' D2O 100 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SUGAR_(3-MER) 2.8 mM 'natural abundance' H2O 95 % . D2O 5 % . stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details 'Glycam_06 force field' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_long_range_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC long range' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH temperature 277 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH temperature 310 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . 'separate tube (no insert) similar to the experimental sample tube' . 1.000000000 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'SUGAR (3-MER)' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 6HH H21 H 2.316 0.005 1 2 1 1 6HH H22 H 2.316 0.005 1 3 1 1 6HH H31 H 1.583 0.005 1 4 1 1 6HH H32 H 1.583 0.005 1 5 1 1 6HH H41 H 1.316 0.005 1 6 1 1 6HH H42 H 1.316 0.005 1 7 1 1 6HH H51 H 1.551 0.005 1 8 1 1 6HH H52 H 1.551 0.005 1 9 1 1 6HH H61 H 3.894 0.005 2 10 1 1 6HH H62 H 3.554 0.005 2 11 1 1 6HH C2 C 37.640 0.050 1 12 1 1 6HH C3 C 27.094 0.050 1 13 1 1 6HH C4 C 27.446 0.050 1 14 1 1 6HH C5 C 30.982 0.050 1 15 1 1 6HH C6 C 73.089 0.050 1 16 2 2 NAG H1 H 4.464 0.005 1 17 2 2 NAG H2 H 3.890 0.005 1 18 2 2 NAG H3 H 3.809 0.005 1 19 2 2 NAG H4 H 3.884 0.005 1 20 2 2 NAG H5 H 3.488 0.005 1 21 2 2 NAG H61 H 3.738 0.005 2 22 2 2 NAG H62 H 3.923 0.005 2 23 2 2 NAG H81 H 2.008 0.005 1 24 2 2 NAG H82 H 2.008 0.005 1 25 2 2 NAG H83 H 2.008 0.005 1 26 2 2 NAG HN2 H 8.526 0.005 1 27 2 2 NAG C1 C 103.670 0.050 1 28 2 2 NAG C2 C 58.327 0.050 1 29 2 2 NAG C3 C 77.511 0.050 1 30 2 2 NAG C4 C 76.215 0.050 1 31 2 2 NAG C5 C 77.897 0.050 1 32 2 2 NAG C6 C 62.502 0.050 1 33 2 2 NAG C8 C 24.850 0.050 1 34 3 3 NAG H1 H 4.516 0.005 1 35 3 3 NAG H2 H 3.747 0.005 1 36 3 3 NAG H3 H 3.523 0.005 1 37 3 3 NAG H4 H 3.228 0.005 1 38 3 3 NAG H5 H 3.420 0.005 1 39 3 3 NAG H61 H 3.959 0.005 2 40 3 3 NAG H62 H 3.599 0.005 2 41 3 3 NAG H81 H 2.038 0.005 1 42 3 3 NAG H82 H 2.038 0.005 1 43 3 3 NAG H83 H 2.038 0.005 1 44 3 3 NAG HN2 H 8.553 0.005 1 45 3 3 NAG C1 C 103.095 0.050 1 46 3 3 NAG C2 C 58.419 0.050 1 47 3 3 NAG C3 C 76.256 0.050 1 48 3 3 NAG C4 C 73.278 0.050 1 49 3 3 NAG C5 C 78.728 0.050 1 50 3 3 NAG C6 C 64.237 0.050 1 51 3 3 NAG C8 C 24.687 0.050 1 52 4 4 FUC H1 H 5.121 0.005 1 53 4 4 FUC H2 H 3.681 0.005 1 54 4 4 FUC H3 H 3.954 0.005 1 55 4 4 FUC H4 H 3.799 0.005 1 56 4 4 FUC H5 H 4.776 0.005 1 57 4 4 FUC H61 H 1.262 0.005 1 58 4 4 FUC H62 H 1.262 0.005 1 59 4 4 FUC H63 H 1.262 0.005 1 60 4 4 FUC C1 C 101.286 0.050 1 61 4 4 FUC C2 C 70.287 0.050 1 62 4 4 FUC C3 C 71.803 0.050 1 63 4 4 FUC C4 C 74.659 0.050 1 64 4 4 FUC C5 C 69.361 0.050 1 65 4 4 FUC C6 C 18.152 0.050 1 stop_ save_ save_assigned_chem_shift_list _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-1H TOCSY' '2D 1H-13C HSQC long range' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'SUGAR (3-MER)' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 6HH H21 H 2.341 0.005 1 2 1 1 6HH H22 H 2.341 0.005 1 3 1 1 6HH H31 H 1.597 0.005 1 4 1 1 6HH H32 H 1.597 0.005 1 5 1 1 6HH H41 H 1.336 0.005 1 6 1 1 6HH H42 H 1.336 0.005 1 7 1 1 6HH H51 H 1.563 0.005 1 8 1 1 6HH H52 H 1.563 0.005 1 9 1 1 6HH H61 H 3.882 0.005 2 10 1 1 6HH H62 H 3.572 0.005 2 11 1 1 6HH C2 C 37.393 0.050 1 12 1 1 6HH C3 C 27.039 0.050 1 13 1 1 6HH C4 C 27.487 0.050 1 14 1 1 6HH C5 C 31.020 0.050 1 15 1 1 6HH C6 C 73.099 0.050 1 16 2 2 NAG H1 H 4.498 0.005 1 17 2 2 NAG H2 H 3.882 0.005 1 18 2 2 NAG H3 H 3.851 0.005 1 19 2 2 NAG H4 H 3.881 0.005 1 20 2 2 NAG H5 H 3.500 0.005 1 21 2 2 NAG H61 H 3.746 0.005 2 22 2 2 NAG H62 H 3.926 0.005 2 23 2 2 NAG H81 H 2.022 0.005 1 24 2 2 NAG H82 H 2.022 0.005 1 25 2 2 NAG H83 H 2.022 0.005 1 26 2 2 NAG C1 C 103.638 0.050 1 27 2 2 NAG C2 C 58.420 0.050 1 28 2 2 NAG C3 C 77.647 0.050 1 29 2 2 NAG C4 C 76.474 0.050 1 30 2 2 NAG C5 C 78.160 0.050 1 31 2 2 NAG C6 C 62.821 0.050 1 32 2 2 NAG C7 C 176.857 0.050 1 33 2 2 NAG C8 C 25.014 0.050 1 34 3 3 NAG H1 H 4.526 0.005 1 35 3 3 NAG H2 H 3.730 0.005 1 36 3 3 NAG H3 H 3.553 0.005 1 37 3 3 NAG H4 H 3.256 0.005 1 38 3 3 NAG H5 H 3.430 0.005 1 39 3 3 NAG H61 H 3.959 0.005 2 40 3 3 NAG H62 H 3.622 0.005 2 41 3 3 NAG H81 H 2.053 0.005 1 42 3 3 NAG H82 H 2.053 0.005 1 43 3 3 NAG H83 H 2.053 0.005 1 44 3 3 NAG C1 C 103.152 0.050 1 45 3 3 NAG C2 C 58.569 0.050 1 46 3 3 NAG C3 C 76.418 0.050 1 47 3 3 NAG C4 C 73.520 0.050 1 48 3 3 NAG C5 C 78.691 0.050 1 49 3 3 NAG C6 C 64.371 0.050 1 50 3 3 NAG C7 C 177.291 0.050 1 51 3 3 NAG C8 C 24.888 0.050 1 52 4 4 FUC H1 H 5.124 0.005 1 53 4 4 FUC H2 H 3.711 0.005 1 54 4 4 FUC H3 H 3.949 0.005 1 55 4 4 FUC H4 H 3.807 0.005 1 56 4 4 FUC H5 H 4.737 0.005 1 57 4 4 FUC H61 H 1.270 0.005 1 58 4 4 FUC H62 H 1.270 0.005 1 59 4 4 FUC H63 H 1.270 0.005 1 60 4 4 FUC C1 C 101.192 0.050 1 61 4 4 FUC C2 C 70.527 0.050 1 62 4 4 FUC C3 C 72.006 0.050 1 63 4 4 FUC C4 C 74.802 0.050 1 64 4 4 FUC C5 C 69.415 0.050 1 65 4 4 FUC C6 C 18.246 0.050 1 stop_ save_