data_28133 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Backbone 1H, 13C, 15N, and CB chemical shift assignments for the PDE6 inhibitory gamma-subunit (1-58) ; _BMRB_accession_number 28133 _BMRB_flat_file_name bmr28133.str _Entry_type original _Submission_date 2020-06-15 _Accession_date 2020-06-15 _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 Gupta Richa . . 2 Liu Yong . . 3 Wang Huanchen . . 4 Nordyke Christopher T. . 5 Puterbaugh Ryan Z. . 6 Varga Krisztina . . 7 Chu Feixia . . 8 Ke Hengming . . 9 Vashisth Harish . . 10 Cote Rick H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 47 "13C chemical shifts" 146 "15N chemical shifts" 47 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-09-16 original BMRB . stop_ _Original_release_date 2020-06-15 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32898583 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gupta Richa . . 2 Liu Yong . . 3 Wang Huanchen . . 4 Nordyke Christopher T. . 5 Puterbaugh Ryan Z. . 6 Cui Wenjun . . 7 Varga Krisztina . . 8 Chu Feixia . . 9 Ke Hengming . . 10 Vashisth Harish . . 11 Cote Rick H. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _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 2020 _Details . loop_ _Keyword PDE6 'inhibitory gamma-subunit' 'solution NMR' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'PDE6 inhibitory gamma-subunit (1-58)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'PDE6 inhibitory gamma-subunit (1-58)' $PDE6_inhibitory_gamma-subunit stop_ _System_molecular_weight 6255.13 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_PDE6_inhibitory_gamma-subunit _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PDE6_inhibitory_gamma-subunit _Molecular_mass 6255.13 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 58 _Mol_residue_sequence ; MSENPTTNLTTGDAPTGPTT PRKGPPKFKQRQTRQFKSKP PKKGVKGFGDDIPGMEGL ; loop_ _Residue_seq_code _Residue_label 1 MET 2 SER 3 GLU 4 ASN 5 PRO 6 THR 7 THR 8 ASN 9 LEU 10 THR 11 THR 12 GLY 13 ASP 14 ALA 15 PRO 16 THR 17 GLY 18 PRO 19 THR 20 THR 21 PRO 22 ARG 23 LYS 24 GLY 25 PRO 26 PRO 27 LYS 28 PHE 29 LYS 30 GLN 31 ARG 32 GLN 33 THR 34 ARG 35 GLN 36 PHE 37 LYS 38 SER 39 LYS 40 PRO 41 PRO 42 LYS 43 LYS 44 GLY 45 VAL 46 LYS 47 GLY 48 PHE 49 GLY 50 ASP 51 ASP 52 ILE 53 PRO 54 GLY 55 MET 56 GLU 57 GLY 58 LEU 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 $PDE6_inhibitory_gamma-subunit chicken 9031 Eukaryota Metazoa Gallus gallus 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 $PDE6_inhibitory_gamma-subunit 'recombinant technology' . Escherichia coli BL21(DE3) pET11a 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 $PDE6_inhibitory_gamma-subunit 50 uM '[U-98% 13C; U-98% 15N]' TRIS 20 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' 'magnesium chloride' 1 mM 'natural abundance' D2O 5 '% v/v' [U-2H] 'sodium azide' 1 mM 'natural abundance' DSS 200 uM '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_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_PINE _Saveframe_category software _Name PINE _Version . loop_ _Vendor _Address _Electronic_address 'Bahrami, Markley, Assadi, and Eghbalnia' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III HD' _Field_strength 700 _Details '5-mm triple resonance inverse TCI CryoProbe' save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance NEO' _Field_strength 700 _Details '5-mm triple resonance inverse TCI CryoProbe' 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_ save_3D_HNCACB_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_HNCO_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_1_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.5 . pH pressure 1 . atm temperature 273 . 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 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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_Pgamma_PDE6_NMRSTAR _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' '3D HNCA' '3D HNCACB' '3D HNCO' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_1_conditions _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'PDE6 inhibitory gamma-subunit (1-58)' _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 3 3 GLU H H 8.614 0.00 . 2 3 3 GLU C C 175.790 0.00 . 3 3 3 GLU CA C 56.347 0.00 . 4 3 3 GLU CB C 30.510 0.00 . 5 3 3 GLU N N 121.761 0.00 . 6 4 4 ASN H H 8.617 0.00 . 7 4 4 ASN CA C 51.383 0.00 . 8 4 4 ASN CB C 38.717 0.00 . 9 4 4 ASN N N 121.187 0.06 . 10 5 5 PRO C C 177.513 0.00 . 11 5 5 PRO CA C 63.206 0.00 . 12 5 5 PRO CB C 32.247 0.00 . 13 6 6 THR H H 8.285 0.02 . 14 6 6 THR C C 174.861 0.00 . 15 6 6 THR CA C 61.956 0.00 . 16 6 6 THR CB C 69.791 0.00 . 17 6 6 THR N N 113.959 0.06 . 18 7 7 THR H H 8.050 0.00 . 19 7 7 THR C C 174.067 0.00 . 20 7 7 THR CA C 61.871 0.01 . 21 7 7 THR CB C 69.802 0.02 . 22 7 7 THR N N 115.907 0.01 . 23 8 8 ASN H H 8.444 0.00 . 24 8 8 ASN C C 174.968 0.00 . 25 8 8 ASN CA C 53.385 0.05 . 26 8 8 ASN CB C 38.739 0.01 . 27 8 8 ASN N N 121.184 0.02 . 28 9 9 LEU H H 8.282 0.00 . 29 9 9 LEU C C 177.707 0.00 . 30 9 9 LEU CA C 55.376 0.01 . 31 9 9 LEU CB C 42.410 0.03 . 32 9 9 LEU N N 122.716 0.01 . 33 10 10 THR H H 8.253 0.00 . 34 10 10 THR C C 174.868 0.00 . 35 10 10 THR CA C 61.808 0.00 . 36 10 10 THR CB C 69.802 0.00 . 37 10 10 THR N N 114.704 0.01 . 38 11 11 THR H H 8.120 0.00 . 39 11 11 THR C C 175.102 0.00 . 40 11 11 THR CA C 61.867 0.01 . 41 11 11 THR CB C 69.779 0.01 . 42 11 11 THR N N 115.361 0.01 . 43 12 12 GLY H H 8.345 0.00 . 44 12 12 GLY C C 173.799 0.00 . 45 12 12 GLY CA C 45.215 0.08 . 46 12 12 GLY N N 110.980 0.01 . 47 13 13 ASP H H 8.208 0.00 . 48 13 13 ASP C C 175.694 0.00 . 49 13 13 ASP CA C 54.145 0.02 . 50 13 13 ASP CB C 41.335 0.01 . 51 13 13 ASP N N 120.352 0.10 . 52 14 14 ALA H H 8.213 0.00 . 53 14 14 ALA CA C 50.543 0.00 . 54 14 14 ALA CB C 18.231 0.00 . 55 14 14 ALA N N 125.207 0.01 . 56 15 15 PRO C C 177.303 0.00 . 57 15 15 PRO CA C 63.213 0.00 . 58 15 15 PRO CB C 32.040 0.00 . 59 16 16 THR H H 8.195 0.00 . 60 16 16 THR C C 174.857 0.00 . 61 16 16 THR CA C 61.599 0.01 . 62 16 16 THR CB C 69.987 0.00 . 63 16 16 THR N N 113.374 0.02 . 64 17 17 GLY H H 8.182 0.00 . 65 17 17 GLY CA C 44.687 0.00 . 66 17 17 GLY N N 111.028 0.02 . 67 18 18 PRO C C 177.233 0.00 . 68 18 18 PRO CA C 63.115 0.00 . 69 18 18 PRO CB C 32.239 0.00 . 70 19 19 THR H H 8.306 0.00 . 71 19 19 THR C C 174.597 0.00 . 72 19 19 THR CA C 61.950 0.01 . 73 19 19 THR CB C 69.723 0.00 . 74 19 19 THR N N 114.010 0.03 . 75 20 20 THR H H 8.096 0.00 . 76 20 20 THR CA C 60.029 0.00 . 77 20 20 THR CB C 69.777 0.00 . 78 20 20 THR N N 119.101 0.02 . 79 21 21 PRO C C 176.810 0.00 . 80 21 21 PRO CA C 63.248 0.00 . 81 21 21 PRO CB C 31.828 0.00 . 82 22 22 ARG H H 8.432 0.00 . 83 22 22 ARG C C 176.344 0.00 . 84 22 22 ARG CA C 56.156 0.05 . 85 22 22 ARG CB C 30.807 0.02 . 86 22 22 ARG N N 121.927 0.03 . 87 23 23 LYS H H 8.393 0.00 . 88 23 23 LYS C C 176.612 0.00 . 89 23 23 LYS CA C 56.171 0.12 . 90 23 23 LYS CB C 33.310 0.06 . 91 23 23 LYS N N 123.350 0.04 . 92 24 24 GLY H H 8.255 0.00 . 93 24 24 GLY CA C 44.372 0.00 . 94 24 24 GLY N N 110.561 0.02 . 95 26 26 PRO C C 176.794 0.00 . 96 26 26 PRO CA C 62.922 0.00 . 97 26 26 PRO CB C 32.075 0.00 . 98 27 27 LYS H H 8.319 0.00 . 99 27 27 LYS C C 176.369 0.00 . 100 27 27 LYS CA C 56.454 0.05 . 101 27 27 LYS CB C 33.061 0.03 . 102 27 27 LYS N N 121.306 0.04 . 103 28 28 PHE H H 8.117 0.00 . 104 28 28 PHE C C 175.485 0.00 . 105 28 28 PHE CA C 57.422 0.02 . 106 28 28 PHE CB C 39.844 0.01 . 107 28 28 PHE N N 120.715 0.02 . 108 29 29 LYS H H 8.236 0.00 . 109 29 29 LYS C C 176.020 0.00 . 110 29 29 LYS CA C 56.212 0.00 . 111 29 29 LYS CB C 33.254 0.10 . 112 29 29 LYS N N 123.514 0.02 . 113 30 30 GLN H H 8.325 0.00 . 114 30 30 GLN C C 175.941 0.00 . 115 30 30 GLN CA C 55.934 0.02 . 116 30 30 GLN CB C 29.677 0.07 . 117 30 30 GLN N N 122.055 0.04 . 118 31 31 ARG H H 8.460 0.00 . 119 31 31 ARG C C 176.244 0.00 . 120 31 31 ARG CA C 56.218 0.01 . 121 31 31 ARG CB C 30.843 0.01 . 122 31 31 ARG N N 123.005 0.01 . 123 32 32 GLN H H 8.511 0.00 . 124 32 32 GLN C C 176.124 0.00 . 125 32 32 GLN CA C 55.805 0.05 . 126 32 32 GLN CB C 29.610 0.00 . 127 32 32 GLN N N 122.193 0.03 . 128 33 33 THR H H 8.264 0.00 . 129 33 33 THR C C 174.489 0.00 . 130 33 33 THR CA C 61.921 0.02 . 131 33 33 THR CB C 69.960 0.02 . 132 33 33 THR N N 116.269 0.03 . 133 34 34 ARG H H 8.367 0.00 . 134 34 34 ARG C C 175.845 0.00 . 135 34 34 ARG CA C 56.191 0.11 . 136 34 34 ARG CB C 30.811 0.02 . 137 34 34 ARG N N 123.359 0.05 . 138 35 35 GLN H H 8.363 0.00 . 139 35 35 GLN C C 175.505 0.00 . 140 35 35 GLN CA C 55.713 0.03 . 141 35 35 GLN CB C 29.596 0.01 . 142 35 35 GLN N N 121.611 0.01 . 143 36 36 PHE H H 8.295 0.00 . 144 36 36 PHE C C 175.500 0.00 . 145 36 36 PHE CA C 57.632 0.06 . 146 36 36 PHE CB C 39.878 0.03 . 147 36 36 PHE N N 121.912 0.08 . 148 37 37 LYS H H 8.294 0.00 . 149 37 37 LYS C C 176.133 0.00 . 150 37 37 LYS CA C 56.298 0.08 . 151 37 37 LYS CB C 33.230 0.04 . 152 37 37 LYS N N 123.242 0.02 . 153 38 38 SER H H 8.226 0.00 . 154 38 38 SER C C 174.007 0.00 . 155 38 38 SER CA C 58.164 0.02 . 156 38 38 SER CB C 63.952 0.00 . 157 38 38 SER N N 117.243 0.01 . 158 39 39 LYS H H 8.336 0.00 . 159 39 39 LYS CA C 54.219 0.00 . 160 39 39 LYS CB C 32.576 0.00 . 161 39 39 LYS N N 124.001 0.01 . 162 41 41 PRO C C 176.742 0.00 . 163 41 41 PRO CA C 62.773 0.00 . 164 41 41 PRO CB C 32.354 0.00 . 165 42 42 LYS H H 8.291 0.00 . 166 42 42 LYS C C 176.370 0.00 . 167 42 42 LYS CA C 56.828 0.60 . 168 42 42 LYS CB C 33.373 0.04 . 169 42 42 LYS N N 121.571 0.04 . 170 43 43 LYS H H 8.358 0.00 . 171 43 43 LYS C C 176.884 0.00 . 172 43 43 LYS CA C 56.605 0.05 . 173 43 43 LYS CB C 33.058 0.11 . 174 43 43 LYS N N 123.041 0.03 . 175 44 44 GLY H H 8.474 0.00 . 176 44 44 GLY C C 174.038 0.00 . 177 44 44 GLY CA C 45.194 0.06 . 178 44 44 GLY N N 110.751 0.04 . 179 45 45 VAL H H 7.954 0.00 . 180 45 45 VAL C C 176.203 0.00 . 181 45 45 VAL CA C 62.129 0.00 . 182 45 45 VAL CB C 32.875 0.01 . 183 45 45 VAL N N 119.229 0.01 . 184 46 46 LYS H H 8.485 0.00 . 185 46 46 LYS C C 177.000 0.00 . 186 46 46 LYS CA C 56.676 0.02 . 187 46 46 LYS CB C 32.918 0.03 . 188 46 46 LYS N N 125.154 0.01 . 189 47 47 GLY H H 8.474 0.00 . 190 47 47 GLY C C 173.767 0.00 . 191 47 47 GLY CA C 45.105 0.07 . 192 47 47 GLY N N 110.798 0.05 . 193 48 48 PHE H H 8.204 0.00 . 194 48 48 PHE C C 176.314 0.00 . 195 48 48 PHE CA C 58.055 0.01 . 196 48 48 PHE CB C 39.668 0.04 . 197 48 48 PHE N N 120.033 0.04 . 198 49 49 GLY H H 8.434 0.00 . 199 49 49 GLY C C 173.847 0.00 . 200 49 49 GLY CA C 45.392 0.00 . 201 49 49 GLY N N 110.861 0.02 . 202 50 50 ASP H H 8.219 0.08 . 203 50 50 ASP C C 175.840 0.00 . 204 50 50 ASP CA C 54.334 0.00 . 205 50 50 ASP CB C 41.289 0.00 . 206 50 50 ASP N N 120.161 0.16 . 207 51 51 ASP H H 8.361 0.00 . 208 51 51 ASP C C 175.687 0.00 . 209 51 51 ASP CA C 54.218 0.03 . 210 51 51 ASP CB C 41.066 0.04 . 211 51 51 ASP N N 119.897 0.01 . 212 52 52 ILE H H 8.023 0.00 . 213 52 52 ILE CA C 58.761 0.00 . 214 52 52 ILE CB C 38.631 0.00 . 215 52 52 ILE N N 122.404 0.02 . 216 53 53 PRO C C 177.562 0.00 . 217 53 53 PRO CA C 63.586 0.00 . 218 53 53 PRO CB C 32.029 0.00 . 219 54 54 GLY H H 8.524 0.00 . 220 54 54 GLY C C 174.589 0.00 . 221 54 54 GLY CA C 45.401 0.00 . 222 54 54 GLY N N 109.529 0.02 . 223 55 55 MET H H 8.162 0.00 . 224 55 55 MET C C 176.357 0.00 . 225 55 55 MET CA C 55.401 0.01 . 226 55 55 MET CB C 32.945 0.08 . 227 55 55 MET N N 119.603 0.02 . 228 56 56 GLU H H 8.616 0.00 . 229 56 56 GLU C C 176.921 0.00 . 230 56 56 GLU CA C 57.163 0.01 . 231 56 56 GLU CB C 29.981 0.01 . 232 56 56 GLU N N 121.792 0.02 . 233 57 57 GLY H H 8.419 0.00 . 234 57 57 GLY C C 173.271 0.00 . 235 57 57 GLY CA C 45.444 0.00 . 236 57 57 GLY N N 110.136 0.02 . 237 58 58 LEU H H 7.671 0.00 . 238 58 58 LEU CA C 56.591 0.00 . 239 58 58 LEU CB C 43.279 0.00 . 240 58 58 LEU N N 126.995 0.03 . stop_ save_