data_18873 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shift assignment for Lewisx with a (CH2)3NH2 spacer ; _BMRB_accession_number 18873 _BMRB_flat_file_name bmr18873.str _Entry_type original _Submission_date 2012-12-04 _Accession_date 2012-12-04 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Chemical shift assignment for Lewisx with a (CH2)3NH2 spacer' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zierke Mirko . . 2 Ernst Beat . . 3 Allain Frederic . . 4 Schubert Mario . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 31 "13C chemical shifts" 22 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-09-26 original author . stop_ _Original_release_date 2013-09-26 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Stabilization of Branched Oligosaccharides: Lewis(x) Benefits from a Nonconventional C-H...O Hydrogen Bond' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24001318 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zierke Mirko . . 2 Smiesko Martin . . 3 Rabbani Said . . 4 Aeschbacher Thomas . . 5 Cutting Brian . . 6 Allain Frederic H.-T. . 7 Schubert Mario . . 8 Ernst Beat . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 135 _Journal_issue 36 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 13464 _Page_last 13472 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Lewisx-sp8 acetate' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Lewisx $Lewisx-sp8 HAc $entity_ACY 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_Lewisx-sp8 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class carbohydrate _Name_common Lewisx-sp8 _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'LewisX is a blood group antigen, other names are CD15 (cluster of differentiation 15) and SSEA-1 (stage specific embryonic antigen)' stop_ _Details ; D-Gal-b1,4-[L-Fuc-a1,3]-D-GlcNAc-b-(CH2)3-NH2 It is a branched carbohydrate, a standard description used e.g. in the literature is Galb1,4[Fuca1,3]GlcNAcb-sp in which Gal stands for D-galactose, Fuc for L-fucose and GlcNAc for N-Acetyl-glucosamine. ; ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence XXXX loop_ _Residue_seq_code _Residue_label 1 SP8a 2 NAG 3 GAL 4 FUC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_SP8a _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common '(CH2)3NH2 spacer' _BMRB_code SP8a _PDB_code . _Standard_residue_derivative . _Molecular_mass . _Mol_paramagnetic . _Details . 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 . ? 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 . ? 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 . ? 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_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 . ? 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 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 0 . ? O6 O6 O . 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 . ? 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 . ? O1 O1 O . 0 . ? O2 O2 O . 0 . ? O3 O3 O . 0 . ? O4 O4 O . 0 . ? O5 O5 O . 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_ ############# # Ligands # ############# save_ACY _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_ACY (ACETIC ACID)" _BMRB_code ACY _PDB_code ACY _Molecular_mass 60.052 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? CH3 CH3 C . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? HXT HXT H . 0 . ? O O O . 0 . ? OXT OXT O . 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 DOUB C O ? ? SING C OXT ? ? SING C CH3 ? ? SING OXT HXT ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Lewisx-sp8 . . . . . . 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 $Lewisx-sp8 'chemical synthesis' . . . . . 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 $Lewisx-sp8 12.5 mM 'natural abundance' $entity_ACY 12.5 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . 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 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_ save_2D_1H-13C_HMQC-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC-COSY' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 293 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 0 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'referenced with external Sucrose/DSS sample' 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 H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 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' '2D 1H-13C HMQC-COSY' 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 Lewisx _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 SP8a H11 H 4.019 0.003 1 2 1 1 SP8a H12 H 3.711 0.006 1 3 1 1 SP8a H21 H 1.948 0.002 2 4 1 1 SP8a H22 H 1.948 0.002 2 5 1 1 SP8a H31 H 3.077 0.002 2 6 1 1 SP8a H32 H 3.077 0.002 2 7 1 1 SP8a C1 C 70.663 0.050 1 8 1 1 SP8a C2 C 29.424 0.050 1 9 1 1 SP8a C3 C 40.327 0.050 1 10 2 2 NAG H1 H 4.525 0.003 1 11 2 2 NAG H2 H 3.943 0.002 1 12 2 2 NAG H3 H 3.863 0.005 1 13 2 2 NAG H4 H 3.934 0.003 1 14 2 2 NAG H5 H 3.602 0.002 1 15 2 2 NAG H81 H 2.042 0.002 1 16 2 2 NAG H82 H 2.042 0.002 1 17 2 2 NAG H83 H 2.042 0.002 1 18 2 2 NAG H61 H 3.866 0.002 1 19 2 2 NAG H62 H 4.011 0.003 1 20 2 2 NAG C1 C 103.742 0.050 1 21 2 2 NAG C2 C 58.513 0.050 1 22 2 2 NAG C3 C 77.557 0.050 1 23 2 2 NAG C4 C 75.979 0.050 1 24 2 2 NAG C5 C 77.996 0.050 1 25 2 2 NAG C6 C 62.396 0.050 1 26 2 2 NAG C8 C 24.926 0.050 1 27 3 3 GAL H1 H 4.457 0.003 1 28 3 3 GAL H2 H 3.502 0.002 1 29 3 3 GAL H3 H 3.653 0.002 1 30 3 3 GAL H4 H 3.896 0.002 1 31 3 3 GAL H5 H 3.603 0.002 1 32 3 3 GAL H61 H 3.725 0.002 2 33 3 3 GAL H62 H 3.725 0.002 2 34 3 3 GAL C1 C 104.524 0.050 1 35 3 3 GAL C2 C 73.753 0.050 1 36 3 3 GAL C3 C 75.173 0.050 1 37 3 3 GAL C4 C 71.072 0.050 1 38 3 3 GAL C5 C 77.669 0.050 1 39 3 3 GAL C6 C 64.290 0.050 1 40 4 4 FUC H1 H 5.128 0.004 1 41 4 4 FUC H2 H 3.698 0.006 1 42 4 4 FUC H3 H 3.902 0.004 1 43 4 4 FUC H4 H 3.794 0.003 1 44 4 4 FUC H5 H 4.838 0.003 1 45 4 4 FUC H61 H 1.178 0.002 1 46 4 4 FUC H62 H 1.178 0.002 1 47 4 4 FUC H63 H 1.178 0.002 1 48 4 4 FUC C1 C 101.367 0.050 1 49 4 4 FUC C2 C 70.354 0.050 1 50 4 4 FUC C3 C 71.919 0.050 1 51 4 4 FUC C4 C 74.602 0.050 1 52 4 4 FUC C5 C 69.474 0.050 1 53 4 4 FUC C6 C 18.049 0.050 1 stop_ save_