data_28129 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; N-formylkynurenine-containing peptide for random coil chemical shifts at pH 2.3 and 7.4 ; _BMRB_accession_number 28129 _BMRB_flat_file_name bmr28129.str _Entry_type original _Submission_date 2020-06-01 _Accession_date 2020-06-01 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'N-formylkynurenine is an oxidation product of tryptophan' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hinterholzer Arthur . . 2 Stanojlovic Vesna . . 3 Cabrele Chiara . . 4 Schubert Mario . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 64 "13C chemical shifts" 46 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-10-05 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 28123 'Methionine sulfoxide-containing peptide (with Gly as succeeding residue)' 28124 '5-Hydroxytryptophan-containing peptide' 28125 'Kynurenine-containing peptide' 28126 'Methionine sulfoxide-containing peptide (with Ala as succeeding residue)' 28127 'Methionine sulfoxide-containing peptide (with Pro as succeeding residue)' 28128 'Methionine sulfone-containing peptide' 28130 'Oxindolylalanine-containing peptide' stop_ _Original_release_date 2020-06-01 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Identification and Quantification of Oxidation Products in Full-Length Biotherapeutic Antibodies by NMR Spectroscopy ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32530275 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hinterholzer Arthur . . 2 Stanojlovic Vesna . . 3 Regl Christof . . 4 Huber Christian G. . 5 Cabrele Chiara . . 6 Schubert Mario . . stop_ _Journal_abbreviation 'Anal. Chem.' _Journal_volume 92 _Journal_issue 14 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9666 _Page_last 9673 _Year 2020 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name NFK_pep _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label NFK_pep $NFK_pep stop_ _System_molecular_weight . _System_physical_state denatured _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_NFK_pep _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common NFK_pep _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ; XGGXGGX ; loop_ _Residue_seq_code _Residue_label 1 ACE 2 GLY 3 GLY 4 NFK 5 GLY 6 GLY 7 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'ACETYL GROUP' _BMRB_code ACE _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CH3 CH3 C . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 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 DOUB C O ? ? SING C CH3 ? ? SING C H ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ save_ save_chem_comp_NFK _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common N'-Formylkynurenine _BMRB_code NFK _PDB_code NFK _Standard_residue_derivative . _Molecular_mass 236.224 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O O O . 0 . ? C C C . 0 . ? OXT OXT O . 0 . ? CA CA C . 0 . ? N N N . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? OD1 OD1 O . 0 . ? CD2 CD2 C . 0 . ? CAJ CAJ C . 0 . ? CAH CAH C . 0 . ? CAG CAG C . 0 . ? CAI CAI C . 0 . ? CAO CAO C . 0 . ? NAL NAL N . 0 . ? CAF CAF C . 0 . ? OAB OAB O . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H13 H13 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 DOUB O C ? ? SING C OXT ? ? SING C CA ? ? DOUB OD1 CG ? ? SING CA CB ? ? SING CA N ? ? SING CG CB ? ? SING CG CD2 ? ? DOUB CD2 CAJ ? ? SING CD2 CAO ? ? SING CAJ CAH ? ? SING NAL CAO ? ? SING NAL CAF ? ? DOUB CAO CAI ? ? DOUB CAH CAG ? ? SING CAI CAG ? ? DOUB CAF OAB ? ? SING OXT H1 ? ? SING CA H2 ? ? SING N H3 ? ? SING N H4 ? ? SING CB H6 ? ? SING CB H7 ? ? SING CAJ H8 ? ? SING CAH H9 ? ? SING CAG H10 ? ? SING CAI H11 ? ? SING NAL H12 ? ? SING CAF H13 ? ? stop_ save_ save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 N HN1 ? ? SING N HN2 ? ? 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 $NFK_pep . . . . . . 'NFK is an oxidation product of tryptophan' 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 $NFK_pep 'chemical synthesis' . . . . . 'peptide was obtained by incubating a chemically synthesized peptide (ACE-GLY-GLY-TRP-GLY-GLY-NH2)with H2O2.' 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 $NFK_pep 4 mM 'natural abundance' urea 7 M '[U-100% 2H]' 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_ ############################# # 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_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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-1H_COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HMBC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _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 2.3 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . M pH 7.4 . pH pressure 1 . atm temperature 298 . 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 . . . 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_cis_pH2_3 _Saveframe_category assigned_chemical_shifts _Details 'cis NFK shifts' loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-13C HMBC' 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 NFK_pep _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 2 2 GLY HA2 H 3.892 0.005 5 2 2 2 GLY HA3 H 3.892 0.005 5 3 2 2 GLY CA C 45.270 0.100 5 4 3 3 GLY HA2 H 4.000 0.005 5 5 3 3 GLY HA3 H 4.000 0.005 5 6 3 3 GLY CA C 45.263 0.100 5 7 4 4 NFK H2 H 5.002 0.005 1 8 4 4 NFK H6 H 3.706 0.005 1 9 4 4 NFK H7 H 3.706 0.005 1 10 4 4 NFK H8 H 8.051 0.005 1 11 4 4 NFK H9 H 7.371 0.005 1 12 4 4 NFK H10 H 7.683 0.005 1 13 4 4 NFK H11 H 7.551 0.005 1 14 4 4 NFK H13 H 8.888 0.005 1 15 4 4 NFK CA C 52.500 0.100 1 16 4 4 NFK CB C 43.774 0.100 1 17 4 4 NFK CG C 204.475 0.100 1 18 4 4 NFK CAF C 167.816 0.100 1 19 4 4 NFK CAG C 138.280 0.100 1 20 4 4 NFK CAH C 127.665 0.100 1 21 4 4 NFK CAI C 120.556 0.100 1 22 4 4 NFK CAJ C 134.505 0.100 1 23 5 5 GLY HA2 H 3.784 0.005 5 24 5 5 GLY HA3 H 3.784 0.005 5 25 5 5 GLY CA C 44.705 0.100 5 26 6 6 GLY HA2 H 3.942 0.005 5 27 6 6 GLY HA3 H 3.942 0.005 5 28 6 6 GLY CA C 44.832 0.100 5 stop_ save_ save_assigned_chem_shift_list_trans_pH2_3 _Saveframe_category assigned_chemical_shifts _Details 'trans NFK' loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-13C HMBC' 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 NFK_pep _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 2 2 GLY HA2 H 3.892 0.005 5 2 2 2 GLY HA3 H 3.892 0.005 5 3 2 2 GLY CA C 45.270 0.100 5 4 3 3 GLY HA2 H 4.000 0.005 5 5 3 3 GLY HA3 H 4.000 0.005 5 6 3 3 GLY CA C 45.263 0.100 5 7 4 4 NFK H2 H 5.002 0.005 1 8 4 4 NFK H6 H 3.706 0.005 1 9 4 4 NFK H7 H 3.706 0.005 1 10 4 4 NFK H8 H 8.010 0.005 1 11 4 4 NFK H9 H 7.364 0.005 1 12 4 4 NFK H10 H 7.679 0.005 1 13 4 4 NFK H11 H 8.246 0.005 1 14 4 4 NFK H13 H 8.387 0.005 1 15 4 4 NFK CA C 52.500 0.100 1 16 4 4 NFK CB C 43.774 0.100 1 17 4 4 NFK CG C 204.475 0.100 1 18 4 4 NFK CAF C 198.706 0.100 1 19 4 4 NFK CAG C 137.676 0.100 1 20 4 4 NFK CAH C 127.665 0.100 1 21 4 4 NFK CAI C 125.434 0.100 1 22 4 4 NFK CAJ C 133.715 0.100 1 23 5 5 GLY HA2 H 3.784 0.005 5 24 5 5 GLY HA3 H 3.784 0.005 5 25 5 5 GLY CA C 44.705 0.100 5 26 6 6 GLY HA2 H 3.942 0.100 5 27 6 6 GLY HA3 H 3.942 0.100 5 28 6 6 GLY CA C 44.832 0.100 5 stop_ save_ save_assigned_chem_shift_list_cis_pH7_4 _Saveframe_category assigned_chemical_shifts _Details 'cis NFK' loop_ _Experiment_label '2D 1H-13C HSQC' 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 NFK_pep _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 2 2 GLY HA2 H 3.790 0.005 1 2 2 2 GLY HA3 H 3.790 0.005 1 3 2 2 GLY CA C 44.712 0.100 1 4 3 3 GLY HA2 H 3.874 0.005 1 5 3 3 GLY HA3 H 3.874 0.005 1 6 3 3 GLY CA C 45.344 0.100 1 7 4 4 NFK H2 H 5.005 0.005 1 8 4 4 NFK H6 H 3.711 0.005 1 9 4 4 NFK H7 H 3.711 0.005 1 10 4 4 NFK H8 H 8.054 0.005 1 11 4 4 NFK H9 H 7.375 0.005 1 12 4 4 NFK H10 H 7.683 0.005 1 13 4 4 NFK H11 H 7.555 0.005 1 14 4 4 NFK H13 H 8.890 0.005 1 15 4 4 NFK CA C 52.428 0.100 1 16 4 4 NFK CB C 43.771 0.100 1 17 4 4 NFK CAF C 167.760 0.100 1 18 4 4 NFK CAG C 138.355 0.100 1 19 4 4 NFK CAH C 127.635 0.100 1 20 4 4 NFK CAI C 120.458 0.100 1 21 4 4 NFK CAJ C 134.538 0.100 1 22 5 5 GLY HA2 H 4.001 0.005 1 23 5 5 GLY HA3 H 4.001 0.005 1 24 5 5 GLY CA C 45.255 0.100 1 25 6 6 GLY HA2 H 3.951 0.001 1 26 6 6 GLY HA3 H 3.951 0.001 1 27 6 6 GLY CA C 44.791 0.100 1 stop_ save_ save_assigned_chem_shift_list_trans_pH7_4 _Saveframe_category assigned_chemical_shifts _Details 'trans NFK' loop_ _Experiment_label '2D 1H-13C HSQC' 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 NFK_pep _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 2 2 GLY HA2 H 3.790 0.001 1 2 2 2 GLY HA3 H 3.790 0.001 1 3 2 2 GLY CA C 44.712 0.100 1 4 3 3 GLY HA2 H 3.874 0.005 1 5 3 3 GLY HA3 H 3.874 0.005 1 6 3 3 GLY CA C 45.344 0.100 1 7 4 4 NFK H2 H 5.005 0.005 1 8 4 4 NFK H6 H 3.711 0.005 1 9 4 4 NFK H7 H 3.711 0.005 1 10 4 4 NFK H8 H 8.013 0.005 1 11 4 4 NFK H9 H 7.368 0.005 1 12 4 4 NFK H10 H 7.678 0.005 1 13 4 4 NFK H11 H 8.246 0.005 1 14 4 4 NFK H13 H 8.388 0.005 1 15 4 4 NFK CA C 52.428 0.100 1 16 4 4 NFK CB C 43.771 0.100 1 17 4 4 NFK CAF C 198.704 0.100 1 18 4 4 NFK CAG C 137.659 0.100 1 19 4 4 NFK CAH C 127.635 0.100 1 20 4 4 NFK CAI C 125.388 0.100 1 21 4 4 NFK CAJ C 133.723 0.100 1 22 5 5 GLY HA2 H 4.001 0.005 1 23 5 5 GLY HA3 H 4.001 0.005 1 24 5 5 GLY CA C 45.255 0.100 1 25 6 6 GLY HA2 H 3.951 0.005 1 26 6 6 GLY HA3 H 3.951 0.005 1 27 6 6 GLY CA C 44.791 0.100 1 stop_ save_