data_27582 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Backbone 1H,15N Chemical Shift Assignments human Pdx1 (146-233) ; _BMRB_accession_number 27582 _BMRB_flat_file_name bmr27582.str _Entry_type original _Submission_date 2018-08-21 _Accession_date 2018-08-21 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Backbone chemical shift assignment for Pdx1 (146-233) obtained from HNCACB and CBCACONH spectra, as well as a published assignment of the Pdx1 DBD (Bastidas and Showalter, 2013) for reference. Spectra were acquired using 300 uM 13C,15N-labeled Pdx1 (146-233) in PBS pH 7.4, 10% D2O, 5 mM -ME. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ostertag Michael S. . 2 Messias Ana C. . 3 Popowicz Grzegorz M. . 4 Sattler Michael . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 72 "15N chemical shifts" 72 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-02-18 update BMRB 'update entry citation' 2018-11-28 original author 'original release' stop_ _Original_release_date 2018-08-24 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The Structure of the SPOP-Pdx1 Interface Reveals Insights into the Phosphorylation-Dependent Binding Regulation ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30449689 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ostertag Michael S. . 2 Messias Ana C. . 3 Sattler Michael . . 4 Popowicz Grzegorz M. . stop_ _Journal_abbreviation Structure _Journal_volume 27 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 327 _Page_last 334 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Pdx1 apo form' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Pdx1 DBD-SBS' $Pdx1 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_Pdx1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Pdx1 _Molecular_mass . _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 92 _Mol_residue_sequence ; GAMGNKRTRTAYTRAQLLEL EKEFLFNKYISRPRRVELAV MLNLTERHIKIWFQNRRMKW KKEEDKKRGGGTAVGGGGVA EPEQDCAVTSGE ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 142 GLY 2 143 ALA 3 144 MET 4 145 GLY 5 146 ASN 6 147 LYS 7 148 ARG 8 149 THR 9 150 ARG 10 151 THR 11 152 ALA 12 153 TYR 13 154 THR 14 155 ARG 15 156 ALA 16 157 GLN 17 158 LEU 18 159 LEU 19 160 GLU 20 161 LEU 21 162 GLU 22 163 LYS 23 164 GLU 24 165 PHE 25 166 LEU 26 167 PHE 27 168 ASN 28 169 LYS 29 170 TYR 30 171 ILE 31 172 SER 32 173 ARG 33 174 PRO 34 175 ARG 35 176 ARG 36 177 VAL 37 178 GLU 38 179 LEU 39 180 ALA 40 181 VAL 41 182 MET 42 183 LEU 43 184 ASN 44 185 LEU 45 186 THR 46 187 GLU 47 188 ARG 48 189 HIS 49 190 ILE 50 191 LYS 51 192 ILE 52 193 TRP 53 194 PHE 54 195 GLN 55 196 ASN 56 197 ARG 57 198 ARG 58 199 MET 59 200 LYS 60 201 TRP 61 202 LYS 62 203 LYS 63 204 GLU 64 205 GLU 65 206 ASP 66 207 LYS 67 208 LYS 68 209 ARG 69 210 GLY 70 211 GLY 71 212 GLY 72 213 THR 73 214 ALA 74 215 VAL 75 216 GLY 76 217 GLY 77 218 GLY 78 219 GLY 79 220 VAL 80 221 ALA 81 222 GLU 82 223 PRO 83 224 GLU 84 225 GLN 85 226 ASP 86 227 CYS 87 228 ALA 88 229 VAL 89 230 THR 90 231 SER 91 232 GLY 92 233 GLU 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 $Pdx1 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 $Pdx1 'recombinant technology' . Escherichia coli 'Rosetta2 DE3' pETM-11 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 $Pdx1 300 uM [U-15N] NaCl 137 mM 'natural abundance' KCl 2.7 mM 'natural abundance' Na2HPO4 10 mM 'natural abundance' KH2PO4 1.8 mM 'natural abundance' beta-ME 5 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details 'Bruker Avance 600 with QCI cryogenic probe' 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_CBCA(CO)NH_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_HNCACB_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _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' 137 . mM 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 'The compound used for referencing is: 3-(Trimethylsilyl)-1-propanesulfonic acid sodium salt.' 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 na direct . . . 1.0 DSS N 15 nitrogen ppm 0 na direct . . . 1.0 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-15N HSQC' 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 'Pdx1 DBD-SBS' _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 1 153 12 TYR H H 7.86198 . 1 2 153 12 TYR N N 117.88372 . 1 3 154 13 THR H H 9.10051 . 1 4 154 13 THR N N 114.32595 . 1 5 155 14 ARG H H 8.85968 . 1 6 155 14 ARG N N 121.38653 . 1 7 156 15 ALA H H 8.32761 . 1 8 156 15 ALA N N 119.27213 . 1 9 157 16 GLN H H 7.64617 . 1 10 157 16 GLN N N 116.69786 . 1 11 158 17 LEU H H 8.25335 . 1 12 158 17 LEU N N 117.66457 . 1 13 159 18 LEU H H 8.10106 . 1 14 159 18 LEU N N 118.55242 . 1 15 160 19 GLU H H 7.19397 . 1 16 160 19 GLU N N 117.71895 . 1 17 161 20 LEU H H 7.95274 . 1 18 161 20 LEU N N 122.11446 . 1 19 162 21 GLU H H 8.09482 . 1 20 162 21 GLU N N 118.15082 . 1 21 163 22 LYS H H 7.53530 . 1 22 163 22 LYS N N 119.41109 . 1 23 164 23 GLU H H 7.82820 . 1 24 164 23 GLU N N 120.32477 . 1 25 165 24 PHE H H 8.66739 . 1 26 165 24 PHE N N 120.70252 . 1 27 166 25 LEU H H 7.81700 . 1 28 166 25 LEU N N 116.65696 . 1 29 167 26 PHE H H 7.31277 . 1 30 167 26 PHE N N 117.20625 . 1 31 168 27 ASN H H 8.50124 . 1 32 168 27 ASN N N 118.47320 . 1 33 169 28 LYS H H 8.00547 . 1 34 169 28 LYS N N 120.87872 . 1 35 170 29 TYR H H 7.61033 . 1 36 170 29 TYR N N 114.78454 . 1 37 171 30 ILE H H 7.42692 . 1 38 171 30 ILE N N 117.35218 . 1 39 172 31 SER H H 8.50309 . 1 40 172 31 SER N N 121.74876 . 1 41 173 32 ARG H H 9.15666 . 1 42 173 32 ARG N N 121.18995 . 1 43 175 34 ARG H H 7.31886 . 1 44 175 34 ARG N N 118.21595 . 1 45 176 35 ARG H H 8.46040 . 1 46 176 35 ARG N N 121.09636 . 1 47 177 36 VAL H H 8.10176 . 1 48 177 36 VAL N N 118.28900 . 1 49 178 37 GLU H H 7.63864 . 1 50 178 37 GLU N N 119.20090 . 1 51 179 38 LEU H H 8.63168 . 1 52 179 38 LEU N N 119.81591 . 1 53 180 39 ALA H H 8.30059 . 1 54 180 39 ALA N N 122.82337 . 1 55 181 40 VAL H H 7.80721 . 1 56 181 40 VAL N N 116.69364 . 1 57 182 41 MET H H 7.99710 . 1 58 182 41 MET N N 119.35361 . 1 59 183 42 LEU H H 8.29390 . 1 60 183 42 LEU N N 114.04026 . 1 61 184 43 ASN H H 7.86254 . 1 62 184 43 ASN N N 117.50888 . 1 63 185 44 LEU H H 8.40015 . 1 64 185 44 LEU N N 119.14024 . 1 65 186 45 THR H H 7.93069 . 1 66 186 45 THR N N 109.40218 . 1 67 187 46 GLU H H 9.22026 . 1 68 187 46 GLU N N 121.34724 . 1 69 188 47 ARG H H 8.17553 . 1 70 188 47 ARG N N 119.42415 . 1 71 189 48 HIS H H 7.96791 . 1 72 189 48 HIS N N 117.30196 . 1 73 190 49 ILE H H 7.83682 . 1 74 190 49 ILE N N 119.57615 . 1 75 191 50 LYS H H 8.60519 . 1 76 191 50 LYS N N 121.54352 . 1 77 192 51 ILE H H 8.53850 . 1 78 192 51 ILE N N 119.13086 . 1 79 193 52 TRP H H 8.27099 . 1 80 193 52 TRP N N 122.02211 . 1 81 194 53 PHE H H 8.88977 . 1 82 194 53 PHE N N 118.55812 . 1 83 195 54 GLN H H 8.05128 . 1 84 195 54 GLN N N 118.79113 . 1 85 196 55 ASN H H 8.27299 . 1 86 196 55 ASN N N 118.70193 . 1 87 197 56 ARG H H 8.48421 . 1 88 197 56 ARG N N 124.20242 . 1 89 198 57 ARG H H 8.32762 . 1 90 198 57 ARG N N 119.47735 . 1 91 199 58 MET H H 7.52896 . 1 92 199 58 MET N N 119.17868 . 1 93 200 59 LYS H H 7.56843 . 1 94 200 59 LYS N N 120.51338 . 1 95 201 60 TRP H H 8.10798 . 1 96 201 60 TRP N N 120.39217 . 1 97 202 61 LYS H H 8.39315 . 1 98 202 61 LYS N N 119.39801 . 1 99 203 62 LYS H H 7.71048 . 1 100 203 62 LYS N N 118.23669 . 1 101 204 63 GLU H H 7.95198 . 1 102 204 63 GLU N N 119.25274 . 1 103 207 66 LYS H H 7.71209 . 1 104 207 66 LYS N N 120.12123 . 1 105 208 67 LYS H H 7.79800 . 1 106 208 67 LYS N N 119.42004 . 1 107 209 68 ARG H H 7.87795 . 1 108 209 68 ARG N N 119.41862 . 1 109 210 69 GLY H H 8.12865 . 1 110 210 69 GLY N N 108.68316 . 1 111 213 72 THR H H 8.07779 . 1 112 213 72 THR N N 113.68029 . 1 113 214 73 ALA H H 8.35103 . 1 114 214 73 ALA N N 126.75707 . 1 115 215 74 VAL H H 8.12494 . 1 116 215 74 VAL N N 119.56093 . 1 117 216 75 GLY H H 8.48029 . 1 118 216 75 GLY N N 112.68465 . 1 119 220 79 VAL H H 7.96050 . 1 120 220 79 VAL N N 119.11854 . 1 121 221 80 ALA H H 8.36564 . 1 122 221 80 ALA N N 128.02498 . 1 123 222 81 GLU H H 8.29949 . 1 124 222 81 GLU N N 121.78155 . 1 125 224 83 GLU H H 8.52301 . 1 126 224 83 GLU N N 121.00499 . 1 127 225 84 GLN H H 8.36886 . 1 128 225 84 GLN N N 121.16962 . 1 129 226 85 ASP H H 8.45166 . 1 130 226 85 ASP N N 121.89181 . 1 131 227 86 CYS H H 8.25997 . 1 132 227 86 CYS N N 119.75164 . 1 133 228 87 ALA H H 8.37340 . 1 134 228 87 ALA N N 126.28379 . 1 135 229 88 VAL H H 8.10621 . 1 136 229 88 VAL N N 119.32239 . 1 137 230 89 THR H H 8.22103 . 1 138 230 89 THR N N 117.67503 . 1 139 231 90 SER H H 8.34957 . 1 140 231 90 SER N N 118.16414 . 1 141 232 91 GLY H H 8.40183 . 1 142 232 91 GLY N N 111.42592 . 1 143 233 92 GLU H H 7.90582 . 1 144 233 92 GLU N N 125.57486 . 1 stop_ save_