data_19748 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of Lactodifucotetraose (LDFT) beta anomer ; _BMRB_accession_number 19748 _BMRB_flat_file_name bmr19748.str _Entry_type original _Submission_date 2014-01-22 _Accession_date 2014-01-22 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schubert Mario . . 2 Allain Frederic H.-T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 30 "13C chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-06-29 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 21031 'described in same manuscript' 21032 'described in same manuscript' 21034 'described in same manuscript' 21053 'described in same manuscript' 21054 'described in same manuscript' stop_ _Original_release_date 2016-06-29 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Fucosylated glycans ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? 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 Allain Frederic H.-T. . 5 Schubert Mario . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Lactodifucotetraose (LDFT) beta anomer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'SUGAR (4-MER)' $SUGAR_(4-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_(4-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class carbohydrate _Name_common SUGAR_(4-MER) _Molecular_mass 634.584 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence ; XXXX ; loop_ _Residue_seq_code _Residue_label 1 BGC 2 GAL 3 FUC 4 FUC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_BGC _Saveframe_category polymer_residue _Mol_type SACCHARIDE _Name_common BETA-D-GLUCOSE _BMRB_code BGC _PDB_code BGC _Standard_residue_derivative . _Molecular_mass 180.156 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C1 C1 C . 0 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 0 . ? O6 O6 O . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6C1 H6C1 H . 0 . ? H6C2 H6C2 H . 0 . ? H1 H1 H . 0 . ? HA HA H . 0 . ? HB HB H . 0 . ? HC HC H . 0 . ? HD HD H . 0 . ? H6 H6 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 C2 C3 ? ? SING C2 C1 ? ? 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 O6 ? ? SING C6 H6C1 ? ? SING C6 H6C2 ? ? SING C1 O1 ? ? SING C1 O5 ? ? SING C1 H1 ? ? SING O1 HA ? ? SING O2 HB ? ? SING O3 HC ? ? SING O4 HD ? ? SING O6 H6 ? ? stop_ save_ save_chem_comp_GAL _Saveframe_category polymer_residue _Mol_type D-SACCHARIDE _Name_common BETA-D-GALACTOSE _BMRB_code GAL _PDB_code GAL _Standard_residue_derivative . _Molecular_mass 180.156 _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 . ? O6 O6 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 . ? HO1 HO1 H . 0 . ? HO2 HO2 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 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 O6 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING O1 HO1 ? ? SING O2 HO2 ? ? 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 _Details $SUGAR_(4-MER) Human 9606 Eukaryota Metazoa Homo sapiens 'this tetrasaccharide is found in human urinary excretion (Chester et al. 1979, Eur. J. Biochem. 100, 385-392)' 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_(4-MER) 'chemical synthesis' . Carbosynth (vendor) . . 'purchased from Carbosynth' 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_(4-MER) 3.2 mM '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 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 '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 Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_900 _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_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 'ionic strength' 0 . M pH 7 . pH pressure 1 . atm temperature 275 . 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 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'SUGAR (4-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 BGC C1 C 98.600 0.050 1 2 1 1 BGC C2 C 78.253 0.050 1 3 1 1 BGC C3 C 79.797 0.050 1 4 1 1 BGC C4 C 75.305 0.050 1 5 1 1 BGC C5 C 78.273 0.050 1 6 1 1 BGC C6 C 62.547 0.050 1 7 1 1 BGC H1 H 4.615 0.005 1 8 1 1 BGC H2 H 3.469 0.005 1 9 1 1 BGC H3 H 3.695 0.005 1 10 1 1 BGC H4 H 3.866 0.005 1 11 1 1 BGC H5 H 3.461 0.005 1 12 1 1 BGC H6C1 H 3.980 0.005 2 13 1 1 BGC H6C2 H 3.785 0.005 2 14 2 2 GAL C1 C 102.831 0.050 1 15 2 2 GAL C2 C 78.877 0.050 1 16 2 2 GAL C3 C 76.259 0.050 1 17 2 2 GAL C4 C 71.447 0.050 1 18 2 2 GAL C5 C 77.619 0.050 1 19 2 2 GAL C6 C 64.269 0.050 1 20 2 2 GAL H1 H 4.494 0.005 1 21 2 2 GAL H2 H 3.628 0.005 1 22 2 2 GAL H3 H 3.842 0.005 1 23 2 2 GAL H4 H 3.839 0.005 1 24 2 2 GAL H5 H 3.577 0.005 1 25 2 2 GAL H61 H 3.740 0.005 2 26 2 2 GAL H62 H 3.704 0.005 2 27 3 3 FUC C1 C 101.959 0.050 1 28 3 3 FUC C2 C 70.823 0.050 1 29 3 3 FUC C3 C 72.298 0.050 1 30 3 3 FUC C4 C 74.301 0.050 1 31 3 3 FUC C5 C 69.586 0.050 1 32 3 3 FUC C6 C 18.108 0.050 1 33 3 3 FUC H1 H 5.286 0.005 1 34 3 3 FUC H2 H 3.774 0.005 1 35 3 3 FUC H3 H 3.774 0.005 1 36 3 3 FUC H4 H 3.811 0.005 1 37 3 3 FUC H5 H 4.259 0.005 1 38 3 3 FUC H61 H 1.260 0.005 1 39 3 3 FUC H62 H 1.260 0.005 1 40 3 3 FUC H63 H 1.260 0.005 1 41 4 4 FUC C1 C 101.044 0.050 1 42 4 4 FUC C2 C 70.680 0.050 1 43 4 4 FUC C3 C 71.785 0.050 1 44 4 4 FUC C4 C 74.614 0.050 1 45 4 4 FUC C5 C 69.422 0.050 1 46 4 4 FUC C6 C 18.129 0.050 1 47 4 4 FUC H1 H 5.447 0.005 1 48 4 4 FUC H2 H 3.790 0.005 1 49 4 4 FUC H3 H 3.969 0.005 1 50 4 4 FUC H4 H 3.810 0.005 1 51 4 4 FUC H5 H 4.885 0.005 1 52 4 4 FUC H61 H 1.238 0.005 1 53 4 4 FUC H62 H 1.238 0.005 1 54 4 4 FUC H63 H 1.238 0.005 1 stop_ save_