data_11172 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 13C and 15N chemical shifts of the membrane-reconstituted subunit c-ring of E. coli H+-ATP synthase ; _BMRB_accession_number 11172 _BMRB_flat_file_name bmr11172.str _Entry_type original _Submission_date 2010-05-14 _Accession_date 2010-05-14 _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 Todokoro Yasuto . . 2 Kobayashi Masatoshi . . 3 Sato Takeshi . . 4 Kawakami Toru . . 5 Yumen Ikuko . . 6 Aimoto Saburo . . 7 Fujiwara Toshimichi . . 8 Akutsu Hideo . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 127 "15N chemical shifts" 35 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-08-03 original BMRB . stop_ _Original_release_date 2010-05-14 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural analysis of the membrane-reconstituted subunit c-ring of E. coli H+-ATP synthase by solid-state NMR ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20596883 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Todokoro Yasuto . . 2 Kobayashi Masatoshi . . 3 Sato Takeshi . . 4 Kawakami Toru . . 5 Yumen Ikuko . . 6 Aimoto Saburo . . 7 Fujiwara Toshimichi . . 8 Akutsu Hideo . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of Biomolecular NMR' _Journal_volume 48 _Journal_issue 1 _Journal_ISSN 0925-2738 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1 _Page_last 11 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'subunit c-ring of FoF1 ATP synthase (EFoc-ring)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'FoF1 ATP synthase subunit c (EFoc)' $entity_1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'From E. coli. The EFoc oligomer takes on a ring structure.' save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'FoF1 ATP synthase subunit c (EFoc)' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 79 _Mol_residue_sequence ; MENLNMDLLYMAAAVMMGLA AIGAAIGIGILGGKFLEGAA RQPDLIPLLRTQFFIVMGLV DAIPMIAVGLGLYVMFAVA ; loop_ _Residue_seq_code _Residue_label 1 MET 2 GLU 3 ASN 4 LEU 5 ASN 6 MET 7 ASP 8 LEU 9 LEU 10 TYR 11 MET 12 ALA 13 ALA 14 ALA 15 VAL 16 MET 17 MET 18 GLY 19 LEU 20 ALA 21 ALA 22 ILE 23 GLY 24 ALA 25 ALA 26 ILE 27 GLY 28 ILE 29 GLY 30 ILE 31 LEU 32 GLY 33 GLY 34 LYS 35 PHE 36 LEU 37 GLU 38 GLY 39 ALA 40 ALA 41 ARG 42 GLN 43 PRO 44 ASP 45 LEU 46 ILE 47 PRO 48 LEU 49 LEU 50 ARG 51 THR 52 GLN 53 PHE 54 PHE 55 ILE 56 VAL 57 MET 58 GLY 59 LEU 60 VAL 61 ASP 62 ALA 63 ILE 64 PRO 65 MET 66 ILE 67 ALA 68 VAL 69 GLY 70 LEU 71 GLY 72 LEU 73 TYR 74 VAL 75 MET 76 PHE 77 ALA 78 VAL 79 ALA 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 _Strain $entity_1 'E. coli' 562 Eubacteria . Escherichia coli MEG119 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 $entity_1 'recombinant technology' . Escherichia coli . pCP35 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type membrane _Details ; The EFoc is in DMPC-d54 bilayers. Protein/lipid molar ratio is 1:40. The sample is hydrated. De-ionized water/total ratio is 10-50%. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $entity_1 6 mg . . '[U-13C; U-15N]' DMPC-d54 21.3 mg . . '2H-hydrocarbon chain' H2O . % 10 50 'natural abundance' NaN3 1 mM . . 'natural abundance' Tris-HCl 10 mM . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type membrane _Details 'The EFoc is in DMPC-d54 bilayers. Protein/lipid molar ratio is 1:40.' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 6 mg '[3-13C]-Ala24, [4-13C]-Asp61' H2O 100 % 'natural abundance' DMPC-d54 21.3 mg '2H-hydrocarbon chain' NaN3 1 mM 'natural abundance' Tris-HCl 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 2007 loop_ _Vendor _Address _Electronic_address 'Felix NMR Inc., San Diego, CA' . . stop_ loop_ _Task 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Infinity-plus _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Infinity-plus _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_Intra-residue_2D_13C-13C_DARR_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'Intra-residue 2D 13C-13C DARR' _Sample_label $sample_1 save_ save_Inter-residue_2D_CACA_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'Inter-residue 2D CACA' _Sample_label $sample_1 save_ save_Intra-residue_2D_NCACB_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'Intra-residue 2D NCACB' _Sample_label $sample_1 save_ save_Inter-residue_2D_N(CO)CACB_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'Inter-residue 2D N(CO)CACB' _Sample_label $sample_1 save_ save_Inter-residue_3D_N(CO)CA_5 _Saveframe_category NMR_applied_experiment _Experiment_name 'Inter-residue 3D N(CO)CA' _Sample_label $sample_1 save_ save_Intra-residue_3D_NCACO_6 _Saveframe_category NMR_applied_experiment _Experiment_name 'Intra-residue 3D NCACO' _Sample_label $sample_1 save_ save_2H-selective_1H-depolarization_13C-NMR(CODSHD)_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2H-selective 1H-depolarization 13C-NMR(CODSHD)' _Sample_label $sample_1 save_ save_13C_rotational_resonance_8 _Saveframe_category NMR_applied_experiment _Experiment_name '13C rotational resonance' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_condition_233K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 8.0 . pH temperature 233 . K stop_ save_ save_condition_223K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 8.0 . pH temperature 223 . K stop_ save_ save_condition_193K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 8.0 . pH temperature 193 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_reference_1 _Saveframe_category chemical_shift_reference _Details ; The 13C chemical shift was referenced to DSS by using the methine carbon signal of adamantane under MAS at 40.5 ppm relative to DSS. The 15N chemical shift was referenced to that of liquid NH3 deduced from the 13C chemical shift using the 15N/13C ratio following the IUPAC recommendation. ; 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 adamantane C 13 'methine carbon' ppm 40.5 external direct . . . 1.0 DSS N 15 'methyl carbon' ppm 0.00 na indirect . . . 0.402979946 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_chemical_shift_1 _Saveframe_category assigned_chemical_shifts _Details 'In the ring structure, the side chain of essential Asp61 takes on the COOH state.' loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label 'Intra-residue 2D 13C-13C DARR' 'Inter-residue 2D CACA' 'Intra-residue 2D NCACB' 'Inter-residue 2D N(CO)CACB' 'Inter-residue 3D N(CO)CA' 'Intra-residue 3D NCACO' '2H-selective 1H-depolarization 13C-NMR(CODSHD)' '13C rotational resonance' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $condition_233K _Chem_shift_reference_set_label $reference_1 _Mol_system_component_name 'FoF1 ATP synthase subunit c (EFoc)' _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 21 21 ALA C C 179 1 1 2 21 21 ALA CA C 55.4 1 1 3 21 21 ALA CB C 18.3 2 1 4 21 21 ALA N N 120 3 1 5 22 22 ILE C C 178 1 1 6 22 22 ILE CA C 66.2 0.9 1 7 22 22 ILE CB C 38.0 1 1 8 22 22 ILE CD1 C 14.7 1.3 1 9 22 22 ILE CG1 C 29.2 1.5 1 10 22 22 ILE CG2 C 17.2 1.4 1 11 22 22 ILE N N 118 2 1 12 23 23 GLY C C 175 1 1 13 23 23 GLY CA C 48.4 0.6 1 14 23 23 GLY N N 107 2 1 15 24 24 ALA C C 179 2 1 16 24 24 ALA CA C 55.3 0.7 1 17 24 24 ALA CB C 18.4 1 1 18 24 24 ALA N N 121 3 1 19 25 25 ALA C C 179 2 1 20 25 25 ALA CA C 55.7 1 1 21 25 25 ALA CB C 18.3 2 1 22 25 25 ALA N N 120 3 1 23 26 26 ILE C C 178 1 1 24 26 26 ILE CA C 66.6 0.9 1 25 26 26 ILE CB C 38.0 1 1 26 26 26 ILE CD1 C 14.7 1.3 1 27 26 26 ILE CG1 C 29.2 1.5 1 28 26 26 ILE CG2 C 17.2 1.4 1 29 26 26 ILE N N 118 5 1 30 27 27 GLY C C 175 1 1 31 27 27 GLY CA C 47.7 0.7 1 32 27 27 GLY N N 107 2 1 33 28 28 ILE C C 178 1 1 34 28 28 ILE CA C 65.9 0.7 1 35 28 28 ILE CB C 38.0 1 1 36 28 28 ILE CD1 C 14.7 1.3 1 37 28 28 ILE CG1 C 29.2 1.5 1 38 28 28 ILE CG2 C 17.2 1.4 1 39 28 28 ILE N N 119 2 1 40 29 29 GLY C C 175 1 1 41 29 29 GLY CA C 47.6 0.7 1 42 29 29 GLY N N 106 2 1 43 30 30 ILE C C 178 1 1 44 30 30 ILE CA C 65.9 0.7 1 45 30 30 ILE CB C 38.0 1 1 46 30 30 ILE CD1 C 14.7 1.3 1 47 30 30 ILE CG1 C 29.2 1.5 1 48 30 30 ILE CG2 C 17.2 1.4 1 49 30 30 ILE N N 120 2 1 50 31 31 LEU C C 179 1 1 51 31 31 LEU CA C 58.5 0.7 1 52 31 31 LEU CB C 41.4 1.4 1 53 31 31 LEU CD1 C 23.4 1.9 2 54 31 31 LEU CD2 C 23.4 1.9 2 55 31 31 LEU CG C 26.8 1.4 1 56 31 31 LEU N N 119 1 1 57 32 32 GLY C C 175 1 1 58 32 32 GLY CA C 47.5 0.7 1 59 32 32 GLY N N 108 2 1 60 33 33 GLY C C 175 1 1 61 33 33 GLY CA C 47.5 0.7 1 62 33 33 GLY N N 108 1 1 63 34 34 LYS C C 179 1 1 64 34 34 LYS CA C 58.0 0.8 1 65 34 34 LYS N N 120 2 1 66 37 37 GLU C C 179 1 1 67 37 37 GLU CA C 59.8 0.7 1 68 37 37 GLU N N 120 2 1 69 38 38 GLY C C 175 1 1 70 38 38 GLY CA C 47.0 0.8 1 71 38 38 GLY N N 108 1 1 72 39 39 ALA C C 179 1 1 73 39 39 ALA CA C 53.6 0.7 1 74 39 39 ALA CB C 18.9 1.5 1 75 39 39 ALA N N 122 3 1 76 42 42 GLN C C 174 1 1 77 42 42 GLN CA C 55.3 0.7 1 78 42 42 GLN N N 120 3 1 79 43 43 PRO CA C 62.0 1 1 80 43 43 PRO N N 134 1 1 81 51 51 THR C C 178 1 1 82 51 51 THR CA C 65.5 1 1 83 51 51 THR CB C 67.3 1 1 84 51 51 THR N N 116 3 1 85 55 55 ILE C C 178 1 1 86 55 55 ILE CA C 65.9 0.6 1 87 55 55 ILE CB C 38.0 1 1 88 55 55 ILE CD1 C 14.7 1.3 1 89 55 55 ILE CG1 C 29.2 1.5 1 90 55 55 ILE CG2 C 17.2 1.4 1 91 55 55 ILE N N 119 3 1 92 56 56 VAL CA C 66.2 0.6 1 93 56 56 VAL CB C 31.3 1 1 94 56 56 VAL CG1 C 22.7 1.7 2 95 56 56 VAL CG2 C 22.7 1.7 2 96 57 57 MET C C 179 1 1 97 57 57 MET CA C 58.7 0.7 1 98 57 57 MET N N 119 3 1 99 58 58 GLY C C 175 1 1 100 58 58 GLY CA C 47.8 0.8 1 101 58 58 GLY N N 107 2 1 102 59 59 LEU C C 179 2 1 103 59 59 LEU CA C 58.2 0.8 1 104 59 59 LEU CB C 41.4 1.4 1 105 59 59 LEU CD1 C 23.4 1.9 2 106 59 59 LEU CD2 C 23.4 1.9 2 107 59 59 LEU CG C 26.8 1.4 1 108 59 59 LEU N N 122 2 1 109 61 61 ASP CG C 179.6 1.2 1 110 67 67 ALA C C 179 2 1 111 67 67 ALA CA C 55.6 0.7 1 112 67 67 ALA CB C 18.3 2 1 113 67 67 ALA N N 119 2 1 114 68 68 VAL C C 178 1 1 115 68 68 VAL CA C 66.4 0.9 1 116 68 68 VAL CB C 31.3 1 1 117 68 68 VAL CG1 C 22.7 1.7 2 118 68 68 VAL CG2 C 22.7 1.7 2 119 68 68 VAL N N 119 3 1 120 69 69 GLY C C 175 1 1 121 69 69 GLY CA C 47.9 0.8 1 122 69 69 GLY N N 108 2 1 123 70 70 LEU C C 179 1 1 124 70 70 LEU CA C 58.2 0.8 1 125 70 70 LEU CB C 41.4 1.4 1 126 70 70 LEU CD1 C 23.4 1.9 2 127 70 70 LEU CD2 C 23.4 1.9 2 128 70 70 LEU CG C 26.8 1.4 1 129 70 70 LEU N N 122 2 1 130 71 71 GLY C C 175 1 1 131 71 71 GLY CA C 47.9 0.8 1 132 71 71 GLY N N 108 2 1 133 72 72 LEU C C 178 1 1 134 72 72 LEU CA C 58.2 0.8 1 135 72 72 LEU CB C 41.4 1.4 1 136 72 72 LEU CD1 C 23.4 1.9 2 137 72 72 LEU CD2 C 23.4 1.9 2 138 72 72 LEU CG C 26.8 1.4 1 139 72 72 LEU N N 122 2 1 140 73 73 TYR C C 178 1 1 141 73 73 TYR CA C 60.4 0.6 1 142 73 73 TYR CB C 41.1 0.6 1 143 73 73 TYR N N 119 3 1 144 74 74 VAL C C 178 1 1 145 74 74 VAL CA C 66.9 0.6 1 146 74 74 VAL CB C 31.3 1 1 147 74 74 VAL CG1 C 22.7 1.7 2 148 74 74 VAL CG2 C 22.7 1.7 2 149 74 74 VAL N N 118 3 1 150 76 76 PHE C C 174 1 1 151 76 76 PHE CA C 59.5 0.7 1 152 76 76 PHE N N 116 1 1 153 77 77 ALA C C 175 1 1 154 77 77 ALA CA C 50.7 0.7 1 155 77 77 ALA CB C 20.0 0.6 1 156 77 77 ALA N N 127 2 1 157 78 78 VAL C C 177 1 1 158 78 78 VAL CA C 61.7 0.7 1 159 78 78 VAL CB C 35.5 1.4 1 160 78 78 VAL CG1 C 21.4 1.4 2 161 78 78 VAL CG2 C 21.4 1.4 2 162 78 78 VAL N N 118 1 1 stop_ save_