data_27804 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Backbone 1H and 15N Chemical Shift Assignments for K11-linked ubiquitin dimer artificially conjugated via propargyl acrylate ; _BMRB_accession_number 27804 _BMRB_flat_file_name bmr27804.str _Entry_type original _Submission_date 2019-02-27 _Accession_date 2019-02-27 _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 Kovermann Michael . . 2 Schneider Tobias . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 70 "15N chemical shifts" 70 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-01-07 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 27802 'Backbone 1H and 15N Chemical Shift Assignments for K11C mutant of ubiquitin including propargyl acrylate linker' 27803 'Backbone 1H and 15N Chemical Shift Assignments for K11C mutant of ubiquitin' 27805 'Backbone 1H and 15N Chemical Shift Assignments for K27C mutant of ubiquitin including propargyl acrylate linker' 27806 'Backbone 1H and 15N Chemical Shift Assignments for K27C mutant of ubiquitin' 27807 'Backbone 1H and 15N Chemical Shift Assignments for K27-linked ubiquitin dimer artificially conjugated via propargyl acrylate' 27808 'Backbone 1H and 15N Chemical Shift Assignments for K63C mutant of ubiquitin including propargyl acrylate linker' 27809 'Backbone 1H and 15N Chemical Shift Assignments for K63C mutant of ubiquitin' 27810 'Backbone 1H and 15N Chemical Shift Assignments for K63-linked ubiquitin dimer artificially conjugated via propargyl acrylate' stop_ _Original_release_date 2019-02-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31882959 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schneider Tobias . . 2 Berg Andrej . . 3 Ulusoy Zeynel . . 4 Gamerdinger Martin . . 5 Peter Christine . . 6 Kovermann Michael . . stop_ _Journal_abbreviation 'Sci. Rep.' _Journal_name_full 'Scientific Reports' _Journal_volume 9 _Journal_issue 1 _Journal_ISSN 2045-2322 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 19991 _Page_last 19991 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Ubiquitin (dimeric)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'K11-linked ubiquitin dimer A' $K11-linked_ubiquitin_dimer 'K11-linked ubiquitin dimer B' $K11-linked_ubiquitin_dimer stop_ _System_molecular_weight 18429 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_K11-linked_ubiquitin_dimer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K11-linked_ubiquitin_dimer _Molecular_mass . _Mol_thiol_state 'all other bound' _Details ; Thiol group of cysteine has been saturated with propargyl acrylate and conjugated with the C-terminus of another unlabeled ubiquitin entity. ; ############################## # Polymer residue sequence # ############################## _Residue_count 76 _Mol_residue_sequence ; MQIFVKTLTGCTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 MET 2 2 GLN 3 3 ILE 4 4 PHE 5 5 VAL 6 6 LYS 7 7 THR 8 8 LEU 9 9 THR 10 10 GLY 11 11 CYS 12 12 THR 13 13 ILE 14 14 THR 15 15 LEU 16 16 GLU 17 17 VAL 18 18 GLU 19 19 PRO 20 20 SER 21 21 ASP 22 22 THR 23 23 ILE 24 24 GLU 25 25 ASN 26 26 VAL 27 27 LYS 28 28 ALA 29 29 LYS 30 30 ILE 31 31 GLN 32 32 ASP 33 33 LYS 34 34 GLU 35 35 GLY 36 36 ILE 37 37 PRO 38 38 PRO 39 39 ASP 40 40 GLN 41 41 GLN 42 42 ARG 43 43 LEU 44 44 ILE 45 45 PHE 46 46 ALA 47 47 GLY 48 48 LYS 49 49 GLN 50 50 LEU 51 51 GLU 52 52 ASP 53 53 GLY 54 54 ARG 55 55 THR 56 56 LEU 57 57 SER 58 58 ASP 59 59 TYR 60 60 ASN 61 61 ILE 62 62 GLN 63 63 LYS 64 64 GLU 65 65 SER 66 66 THR 67 67 LEU 68 68 HIS 69 69 LEU 70 70 VAL 71 71 LEU 72 72 ARG 73 73 LEU 74 74 ARG 75 75 GLY 76 76 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $K11-linked_ubiquitin_dimer Human 9606 Eukaryota Metazoa Homo sapiens 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 $K11-linked_ubiquitin_dimer 'recombinant technology' . Escherichia coli . pET3a/pGEX2TK 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 $K11-linked_ubiquitin_dimer 0.4 mM '[U-99% 13C; U-99% 15N]' 'sodium phosphate' 20 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' collection 'data analysis' processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_3D_HNCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _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 6.8 . 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 water H 1 protons ppm 4.7 internal direct . . . 1 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_ _Software_label $TOPSPIN stop_ loop_ _Experiment_label '2D 1H-15N HSQC' '3D HNCA' 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 'K11-linked ubiquitin dimer A' _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 GLN H H 8.882 0.000 1 2 2 2 GLN N N 122.993 0.000 1 3 3 3 ILE H H 8.221 0.000 1 4 3 3 ILE N N 115.080 0.000 1 5 4 4 PHE H H 8.488 0.000 1 6 4 4 PHE N N 118.573 0.000 1 7 5 5 VAL H H 9.187 0.000 1 8 5 5 VAL N N 121.496 0.000 1 9 6 6 LYS H H 8.895 0.000 1 10 6 6 LYS N N 127.627 0.000 1 11 7 7 THR H H 8.501 0.000 1 12 7 7 THR N N 114.723 0.000 1 13 8 8 LEU H H 9.035 0.000 1 14 8 8 LEU N N 121.139 0.000 1 15 9 9 THR H H 7.573 0.000 1 16 9 9 THR N N 106.026 0.000 1 17 10 10 GLY H H 7.688 0.000 1 18 10 10 GLY N N 108.521 0.000 1 19 11 11 CYS H H 7.243 0.000 1 20 11 11 CYS N N 120.641 0.000 1 21 12 12 THR H H 8.577 0.000 1 22 12 12 THR N N 121.068 0.000 1 23 13 13 ILE H H 9.429 0.000 1 24 13 13 ILE N N 127.270 0.000 1 25 14 14 THR H H 8.666 0.000 1 26 14 14 THR N N 121.709 0.000 1 27 15 15 LEU H H 8.603 0.000 1 28 15 15 LEU N N 125.060 0.000 1 29 16 16 GLU H H 8.018 0.000 1 30 16 16 GLU N N 122.494 0.000 1 31 17 17 VAL H H 8.857 0.000 1 32 17 17 VAL N N 117.574 0.000 1 33 18 18 GLU H H 8.552 0.000 1 34 18 18 GLU N N 119.214 0.000 1 35 20 20 SER H H 6.925 0.000 1 36 20 20 SER N N 103.388 0.000 1 37 21 21 ASP H H 7.954 0.000 1 38 21 21 ASP N N 123.920 0.000 1 39 22 22 THR H H 7.789 0.000 1 40 22 22 THR N N 109.020 0.000 1 41 23 23 ILE H H 8.425 0.000 1 42 23 23 ILE N N 121.211 0.000 1 43 25 25 ASN H H 7.840 0.000 1 44 25 25 ASN N N 121.353 0.000 1 45 26 26 VAL H H 8.018 0.000 1 46 26 26 VAL N N 122.209 0.000 1 47 27 27 LYS H H 8.425 0.000 1 48 27 27 LYS N N 118.858 0.000 1 49 28 28 ALA H H 7.891 0.000 1 50 28 28 ALA N N 123.349 0.000 1 51 29 29 LYS H H 7.802 0.000 1 52 29 29 LYS N N 120.284 0.000 1 53 30 30 ILE H H 8.145 0.000 1 54 30 30 ILE N N 121.496 0.000 1 55 31 31 GLN H H 8.387 0.000 1 56 31 31 GLN N N 123.420 0.000 1 57 32 32 ASP H H 7.993 0.000 1 58 32 32 ASP N N 119.785 0.000 1 59 33 33 LYS H H 7.357 0.000 1 60 33 33 LYS N N 115.579 0.000 1 61 34 34 GLU H H 8.476 0.000 1 62 34 34 GLU N N 113.369 0.000 1 63 35 35 GLY H H 8.387 0.000 1 64 35 35 GLY N N 108.664 0.000 1 65 36 36 ILE H H 6.048 0.000 1 66 36 36 ILE N N 119.999 0.000 1 67 39 39 ASP H H 8.437 0.000 1 68 39 39 ASP N N 113.583 0.000 1 69 40 40 GLN H H 7.700 0.000 1 70 40 40 GLN N N 117.005 0.000 1 71 41 41 GLN H H 7.370 0.000 1 72 41 41 GLN N N 117.860 0.000 1 73 42 42 ARG H H 8.387 0.000 1 74 42 42 ARG N N 122.922 0.000 1 75 43 43 LEU H H 8.692 0.000 1 76 43 43 LEU N N 124.276 0.000 1 77 44 44 ILE H H 9.047 0.000 1 78 44 44 ILE N N 122.565 0.000 1 79 45 45 PHE H H 8.730 0.000 1 80 45 45 PHE N N 124.918 0.000 1 81 46 46 ALA H H 8.895 0.000 1 82 46 46 ALA N N 132.973 0.000 1 83 47 47 GLY H H 8.031 0.000 1 84 47 47 GLY N N 102.461 0.000 1 85 48 48 LYS H H 7.853 0.000 1 86 48 48 LYS N N 121.995 0.000 1 87 49 49 GLN H H 8.577 0.000 1 88 49 49 GLN N N 123.206 0.000 1 89 50 50 LEU H H 8.488 0.000 1 90 50 50 LEU N N 125.773 0.000 1 91 51 51 GLU H H 8.310 0.000 1 92 51 51 GLU N N 123.135 0.000 1 93 52 52 ASP H H 8.082 0.000 1 94 52 52 ASP N N 120.426 0.000 1 95 54 54 ARG H H 7.357 0.000 1 96 54 54 ARG N N 119.357 0.000 1 97 55 55 THR H H 8.730 0.000 1 98 55 55 THR N N 108.735 0.000 1 99 56 56 LEU H H 8.056 0.000 1 100 56 56 LEU N N 118.002 0.000 1 101 57 57 SER H H 8.387 0.000 1 102 57 57 SER N N 113.511 0.000 1 103 58 58 ASP H H 7.853 0.000 1 104 58 58 ASP N N 124.561 0.000 1 105 59 59 TYR H H 7.154 0.000 1 106 59 59 TYR N N 115.792 0.000 1 107 60 60 ASN H H 8.056 0.000 1 108 60 60 ASN N N 115.935 0.000 1 109 61 61 ILE H H 7.167 0.000 1 110 61 61 ILE N N 118.929 0.000 1 111 62 62 GLN H H 7.535 0.000 1 112 62 62 GLN N N 124.918 0.000 1 113 63 63 LYS H H 8.399 0.000 1 114 63 63 LYS N N 120.569 0.000 1 115 64 64 GLU H H 9.225 0.000 1 116 64 64 GLU N N 114.723 0.000 1 117 65 65 SER H H 7.586 0.000 1 118 65 65 SER N N 114.937 0.000 1 119 66 66 THR H H 8.615 0.000 1 120 66 66 THR N N 117.361 0.000 1 121 67 67 LEU H H 9.314 0.000 1 122 67 67 LEU N N 127.840 0.000 1 123 68 68 HIS H H 9.136 0.000 1 124 68 68 HIS N N 119.714 0.000 1 125 69 69 LEU H H 8.183 0.000 1 126 69 69 LEU N N 123.990 0.000 1 127 70 70 VAL H H 9.073 0.000 1 128 70 70 VAL N N 127.270 0.000 1 129 71 71 LEU H H 8.158 0.000 1 130 71 71 LEU N N 123.919 0.000 1 131 72 72 ARG H H 8.514 0.000 1 132 72 72 ARG N N 123.991 0.000 1 133 73 73 LEU H H 8.259 0.000 1 134 73 73 LEU N N 124.205 0.000 1 135 74 74 ARG H H 8.361 0.000 1 136 74 74 ARG N N 121.995 0.000 1 137 75 75 GLY H H 8.425 0.000 1 138 75 75 GLY N N 111.158 0.000 1 139 76 76 GLY H H 7.866 0.000 1 140 76 76 GLY N N 115.008 0.000 1 stop_ save_