data_21054 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the amphibian egg glycan Bv9 from Bombina variegata ; _BMRB_accession_number 21054 _BMRB_flat_file_name bmr21054.str _Entry_type new _Submission_date 2014-01-24 _Accession_date 2014-01-31 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details GLcNAc-beta1,3-[Fuc-alpha1,4-]-GlcNAc-beta-O-CH2-C(OH)H-CH=CH-C(OH)H-CH2-OH loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schubert Mario . . 2 Allain Frederic . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 38 "13C chemical shifts" 28 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]' 21032 'Solution structure of 1,3-Fucosylated chitobiose' 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)' stop_ _Original_release_date 2014-01-30 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 Bv9(trisaccharide) _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Bv9 $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 _Name_common SUGAR_(3-MER) _Molecular_mass . _Mol_thiol_state 'not present' _Details 'The glycan is mentioned as "Bv9" in Coppin et al. 2003, Biochinmie 85, 53-64.' ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence ; XXXX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 0 SP 2 1 MAG 3 2 NAG 4 3 FUC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_MAG _Saveframe_category polymer_residue _Mol_type D-SACCHARIDE _Name_common BETA-METHYL-N-ACETYL-D-GLUCOSAMINE _BMRB_code MAG _PDB_code MAG _Standard_residue_derivative . _Molecular_mass 235.234 _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 . ? CM CM C . 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 . ? HO3 HO3 H . 0 . ? HO4 HO4 H . 0 . ? HO6 HO6 H . 0 . ? HM1 HM1 H . 0 . ? HM2 HM2 H . 0 . ? HM3 HM3 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 CM ? ? SING O3 HO3 ? ? SING O4 HO4 ? ? SING O6 HO6 ? ? SING CM HM1 ? ? SING CM HM2 ? ? SING CM HM3 ? ? stop_ save_ 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) . 191472 Eukaryota Metazoa Bombina variegata 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 _Details $SUGAR_(3-MER) 'obtained from a collaborator' . . . . . 'The experimental sample was a generous gift from GlycoBase, Emmanuel Maes and Yann Guerardel (glycobase.univ-lille1.fr)' 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) 1 mM 'natural abundance' D2O 100 % 'natural abundance' 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) 1 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' 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' 'peak picking' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'geometry optimization' 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 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 273 . 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-13C HSQC' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' 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 Bv9 _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 0 1 SP H11 H 3.594 0.005 2 2 0 1 SP H12 H 3.503 0.005 2 3 0 1 SP H2 H 4.231 0.005 1 4 0 1 SP H3 H 5.764 0.005 4 5 0 1 SP H4 H 5.762 0.009 4 6 0 1 SP H5 H 4.321 0.009 1 7 0 1 SP H61 H 3.892 0.005 2 8 0 1 SP H62 H 3.500 0.005 2 9 0 1 SP C1 C 67.505 0.050 1 10 0 1 SP C2 C 74.651 0.050 1 11 0 1 SP C3 C 133.696 0.050 4 12 0 1 SP C4 C 133.696 0.050 4 13 0 1 SP C5 C 73.154 0.050 1 14 0 1 SP C6 C 75.978 0.050 1 15 1 2 MAG H1 H 4.443 0.005 1 16 1 2 MAG H2 H 3.849 0.005 1 17 1 2 MAG H3 H 3.974 0.005 1 18 1 2 MAG H4 H 3.728 0.005 1 19 1 2 MAG H5 H 3.501 0.005 1 20 1 2 MAG H61 H 3.956 0.005 2 21 1 2 MAG H62 H 3.865 0.005 2 22 1 2 MAG H81 H 2.081 0.005 1 23 1 2 MAG H82 H 2.081 0.005 1 24 1 2 MAG H83 H 2.081 0.005 1 25 1 2 MAG HN2 H 8.498 0.005 1 26 1 2 MAG C1 C 104.535 0.050 1 27 1 2 MAG C2 C 58.332 0.050 1 28 1 2 MAG C3 C 78.768 0.050 1 29 1 2 MAG C4 C 74.956 0.070 1 30 1 2 MAG C5 C 77.917 0.050 1 31 1 2 MAG C6 C 62.223 0.050 1 32 1 2 MAG C7 C 176.835 0.050 1 33 1 2 MAG C8 C 25.026 0.050 1 34 2 3 NAG H1 H 4.621 0.005 1 35 2 3 NAG H2 H 3.629 0.005 1 36 2 3 NAG H3 H 3.587 0.005 1 37 2 3 NAG H4 H 3.188 0.005 1 38 2 3 NAG H5 H 3.386 0.005 1 39 2 3 NAG H61 H 3.974 0.005 2 40 2 3 NAG H62 H 3.572 0.005 2 41 2 3 NAG H81 H 1.990 0.005 1 42 2 3 NAG H82 H 1.990 0.005 1 43 2 3 NAG H83 H 1.990 0.005 1 44 2 3 NAG HN2 H 8.095 0.005 1 45 2 3 NAG C1 C 103.939 0.050 1 46 2 3 NAG C2 C 58.685 0.050 1 47 2 3 NAG C3 C 75.671 0.050 1 48 2 3 NAG C4 C 73.383 0.050 1 49 2 3 NAG C5 C 78.485 0.050 1 50 2 3 NAG C6 C 64.384 0.050 1 51 2 3 NAG C7 C 177.393 0.050 1 52 2 3 NAG C8 C 25.020 0.050 1 53 3 4 FUC H1 H 5.022 0.005 1 54 3 4 FUC H2 H 3.795 0.005 1 55 3 4 FUC H3 H 3.916 0.005 1 56 3 4 FUC H4 H 3.796 0.005 1 57 3 4 FUC H5 H 4.853 0.005 1 58 3 4 FUC H61 H 1.274 0.005 1 59 3 4 FUC H62 H 1.274 0.005 1 60 3 4 FUC H63 H 1.274 0.005 1 61 3 4 FUC C1 C 100.791 0.050 1 62 3 4 FUC C2 C 70.356 0.050 1 63 3 4 FUC C3 C 71.714 0.050 1 64 3 4 FUC C4 C 74.705 0.050 1 65 3 4 FUC C5 C 69.434 0.050 1 66 3 4 FUC C6 C 18.250 0.050 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity 4,5 11,12 stop_ save_