data_19892 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; REFINED STRUCTURE OF OUTER MEMBRANE PROTEIN X IN NANODISC BY MEASURING RESIDUAL DIPOLAR COUPLINGS ; _BMRB_accession_number 19892 _BMRB_flat_file_name bmr19892.str _Entry_type original _Submission_date 2014-04-05 _Accession_date 2014-04-05 _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 Bibow S. . . 2 Carneiro M. G. . 3 Sabo T. M. . 4 Schwiegk C. . . 5 Becker S. . . 6 Riek R. . . 7 Lee D. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 118 "15N chemical shifts" 117 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-03-16 original BMRB . stop_ _Original_release_date 2014-04-14 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title ; Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24752984 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bibow S. . . 2 Carneiro M. G. . 3 Sabo T. M. . 4 Schwiegk C. . . 5 Becker S. . . 6 Riek R. . . 7 Lee D. . . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_volume 23 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last 851 _Year 856 _Details 2014 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'OUTER MEMBRANE PROTEIN X IN NANODISC' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'OUTER MEMBRANE PROTEIN X' $OUTER_MEMBRANE_PROTEIN_X 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_OUTER_MEMBRANE_PROTEIN_X _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common OUTER_MEMBRANE_PROTEIN_X _Molecular_mass 16371.898 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 148 _Mol_residue_sequence ; ATSTVTGGYAQSDAQGQMNK MGGFNLKYRYEEDNSPLGVI GSFTYTEKSRTASSGDYNKN QYYGITAGPAYRINDWASIY GVVGVGYGKFQTTEYPTYKN DTSDYGFSYGAGLQFNPMEN VALDFSYEQSRIRSVDVGTW IAGVGYRF ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 THR 3 SER 4 THR 5 VAL 6 THR 7 GLY 8 GLY 9 TYR 10 ALA 11 GLN 12 SER 13 ASP 14 ALA 15 GLN 16 GLY 17 GLN 18 MET 19 ASN 20 LYS 21 MET 22 GLY 23 GLY 24 PHE 25 ASN 26 LEU 27 LYS 28 TYR 29 ARG 30 TYR 31 GLU 32 GLU 33 ASP 34 ASN 35 SER 36 PRO 37 LEU 38 GLY 39 VAL 40 ILE 41 GLY 42 SER 43 PHE 44 THR 45 TYR 46 THR 47 GLU 48 LYS 49 SER 50 ARG 51 THR 52 ALA 53 SER 54 SER 55 GLY 56 ASP 57 TYR 58 ASN 59 LYS 60 ASN 61 GLN 62 TYR 63 TYR 64 GLY 65 ILE 66 THR 67 ALA 68 GLY 69 PRO 70 ALA 71 TYR 72 ARG 73 ILE 74 ASN 75 ASP 76 TRP 77 ALA 78 SER 79 ILE 80 TYR 81 GLY 82 VAL 83 VAL 84 GLY 85 VAL 86 GLY 87 TYR 88 GLY 89 LYS 90 PHE 91 GLN 92 THR 93 THR 94 GLU 95 TYR 96 PRO 97 THR 98 TYR 99 LYS 100 ASN 101 ASP 102 THR 103 SER 104 ASP 105 TYR 106 GLY 107 PHE 108 SER 109 TYR 110 GLY 111 ALA 112 GLY 113 LEU 114 GLN 115 PHE 116 ASN 117 PRO 118 MET 119 GLU 120 ASN 121 VAL 122 ALA 123 LEU 124 ASP 125 PHE 126 SER 127 TYR 128 GLU 129 GLN 130 SER 131 ARG 132 ILE 133 ARG 134 SER 135 VAL 136 ASP 137 VAL 138 GLY 139 THR 140 TRP 141 ILE 142 ALA 143 GLY 144 VAL 145 GLY 146 TYR 147 ARG 148 PHE 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 _Gene_mnemonic $OUTER_MEMBRANE_PROTEIN_X 'E. coli' 562 Bacteria . Escherichia coli 'OMPX, YBIG, B0814, JW0799' 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 $OUTER_MEMBRANE_PROTEIN_X 'recombinant technology' . ESCHERICHIA COLI 'BL21 (DE3)' PET3b stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '10 MM TRIS-HCL, 100 MM NACL, 1 MM EDTA, 0.05 % SODIUM AZIDE, 0.5 MM' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $OUTER_MEMBRANE_PROTEIN_X 0.5 mM '[U-100% 13C; U-100% 15N]' Tris-HCl 10 mM 'natural abundance' 'sodium azide' 0.05 % 'natural abundance' NaCl 100 mM 'natural abundance' EDTA 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-_PLOR_NIH _Saveframe_category software _Name X-_PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'SCHWIETERS, KUSZEWSKI, TJ' . . stop_ loop_ _Task refinement 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 'structure solution' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer BRUKER _Model 'AVANCE I and AVANCE III' _Field_strength '700. 800, 900' _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_1H-15N_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_1 save_ save_3D_HNCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_COCAINE_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N COCAINE' _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' 100 . mM pH 7.4 . pH pressure 1 . atm temperature 318 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_none _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 na H 1 protons ppm 0 na direct . . . 1.0 na 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 '3D 1H-15N NOESY' '3D HNCA' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $none _Mol_system_component_name 'OUTER MEMBRANE PROTEIN X' _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 THR H H 8.530 . . 2 2 2 THR N N 115.120 . . 3 3 3 SER H H 9.031 . . 4 3 3 SER N N 123.587 . . 5 4 4 THR H H 8.556 . . 6 4 4 THR N N 116.754 . . 7 5 5 VAL H H 8.817 . . 8 5 5 VAL N N 128.336 . . 9 6 6 THR H H 8.968 . . 10 6 6 THR N N 115.974 . . 11 7 7 GLY H H 8.766 . . 12 7 7 GLY N N 105.889 . . 13 8 8 GLY H H 9.126 . . 14 8 8 GLY N N 105.854 . . 15 9 9 TYR H H 8.308 . . 16 9 9 TYR N N 121.078 . . 17 11 11 GLN H H 8.262 . . 18 11 11 GLN N N 121.317 . . 19 12 12 SER H H 9.194 . . 20 12 12 SER N N 123.836 . . 21 13 13 ASP H H 9.099 . . 22 13 13 ASP N N 124.275 . . 23 14 14 ALA H H 8.660 . . 24 14 14 ALA N N 128.864 . . 25 15 15 GLN H H 8.316 . . 26 16 16 GLY H H 8.701 . . 27 16 16 GLY N N 112.489 . . 28 17 17 GLN H H 8.111 . . 29 17 17 GLN N N 119.022 . . 30 18 18 MET H H 8.657 . . 31 18 18 MET N N 120.328 . . 32 19 19 ASN H H 8.009 . . 33 19 19 ASN N N 117.284 . . 34 20 20 LYS H H 8.548 . . 35 20 20 LYS N N 121.136 . . 36 21 21 MET H H 8.618 . . 37 21 21 MET N N 119.903 . . 38 22 22 GLY H H 8.501 . . 39 22 22 GLY N N 111.196 . . 40 23 23 GLY H H 8.092 . . 41 23 23 GLY N N 109.325 . . 42 24 24 PHE H H 9.306 . . 43 24 24 PHE N N 120.147 . . 44 25 25 ASN H H 8.516 . . 45 25 25 ASN N N 118.392 . . 46 26 26 LEU H H 9.381 . . 47 26 26 LEU N N 125.392 . . 48 27 27 LYS H H 8.886 . . 49 27 27 LYS N N 117.292 . . 50 28 28 TYR H H 8.358 . . 51 28 28 TYR N N 120.230 . . 52 29 29 ARG H H 8.503 . . 53 29 29 ARG N N 129.080 . . 54 30 30 TYR H H 8.891 . . 55 30 30 TYR N N 126.838 . . 56 31 31 GLU H H 8.202 . . 57 31 31 GLU N N 128.005 . . 58 32 32 GLU H H 9.137 . . 59 32 32 GLU N N 122.404 . . 60 33 33 ASP H H 8.599 . . 61 33 33 ASP N N 121.672 . . 62 35 35 SER H H 7.363 . . 63 35 35 SER N N 113.001 . . 64 37 37 LEU H H 8.027 . . 65 37 37 LEU N N 123.171 . . 66 38 38 GLY H H 9.050 . . 67 38 38 GLY N N 115.826 . . 68 39 39 VAL H H 8.082 . . 69 39 39 VAL N N 117.450 . . 70 40 40 ILE H H 9.229 . . 71 40 40 ILE N N 125.944 . . 72 41 41 GLY H H 9.112 . . 73 41 41 GLY N N 111.187 . . 74 42 42 SER H H 9.282 . . 75 42 42 SER N N 116.459 . . 76 43 43 PHE H H 9.335 . . 77 43 43 PHE N N 128.932 . . 78 44 44 THR H H 8.685 . . 79 44 44 THR N N 126.670 . . 80 45 45 TYR H H 8.176 . . 81 45 45 TYR N N 125.515 . . 82 46 46 THR H H 8.574 . . 83 46 46 THR N N 117.315 . . 84 47 47 GLU H H 8.338 . . 85 47 47 GLU N N 111.930 . . 86 49 49 SER H H 8.611 . . 87 49 49 SER N N 123.107 . . 88 52 52 ALA H H 8.512 . . 89 52 52 ALA N N 127.376 . . 90 55 55 GLY H H 8.245 . . 91 55 55 GLY N N 110.790 . . 92 56 56 ASP H H 7.848 . . 93 56 56 ASP N N 120.332 . . 94 57 57 TYR H H 8.313 . . 95 57 57 TYR N N 121.702 . . 96 58 58 ASN H H 8.360 . . 97 58 58 ASN N N 122.198 . . 98 59 59 LYS H H 8.276 . . 99 59 59 LYS N N 121.010 . . 100 60 60 ASN H H 8.397 . . 101 60 60 ASN N N 123.086 . . 102 61 61 GLN H H 8.499 . . 103 61 61 GLN N N 120.020 . . 104 62 62 TYR H H 8.650 . . 105 62 62 TYR N N 123.137 . . 106 63 63 TYR H H 8.381 . . 107 63 63 TYR N N 123.929 . . 108 64 64 GLY H H 8.704 . . 109 64 64 GLY N N 106.738 . . 110 65 65 ILE H H 9.140 . . 111 65 65 ILE N N 128.892 . . 112 66 66 THR H H 9.025 . . 113 66 66 THR N N 115.392 . . 114 67 67 ALA H H 9.387 . . 115 67 67 ALA N N 118.885 . . 116 68 68 GLY H H 9.016 . . 117 68 68 GLY N N 103.875 . . 118 70 70 ALA H H 7.875 . . 119 70 70 ALA N N 120.214 . . 120 71 71 TYR H H 9.786 . . 121 71 71 TYR N N 125.130 . . 122 72 72 ARG H H 8.860 . . 123 72 72 ARG N N 131.150 . . 124 73 73 ILE H H 8.475 . . 125 73 73 ILE N N 129.066 . . 126 77 77 ALA H H 7.817 . . 127 77 77 ALA N N 124.611 . . 128 78 78 SER H H 8.195 . . 129 78 78 SER N N 112.605 . . 130 79 79 ILE H H 9.072 . . 131 79 79 ILE N N 119.871 . . 132 80 80 TYR H H 8.439 . . 133 80 80 TYR N N 119.773 . . 134 81 81 GLY H H 8.135 . . 135 81 81 GLY N N 105.795 . . 136 82 82 VAL H H 8.553 . . 137 82 82 VAL N N 111.057 . . 138 83 83 VAL H H 9.021 . . 139 83 83 VAL N N 113.157 . . 140 84 84 GLY H H 8.593 . . 141 84 84 GLY N N 107.838 . . 142 85 85 VAL H H 8.977 . . 143 85 85 VAL N N 122.494 . . 144 86 86 GLY H H 8.871 . . 145 86 86 GLY N N 113.663 . . 146 87 87 TYR H H 9.213 . . 147 87 87 TYR N N 123.276 . . 148 89 89 LYS H H 8.130 . . 149 89 89 LYS N N 122.370 . . 150 91 91 GLN H H 8.374 . . 151 91 91 GLN N N 121.297 . . 152 95 95 TYR H H 8.263 . . 153 95 95 TYR N N 123.254 . . 154 98 98 TYR H H 8.110 . . 155 98 98 TYR N N 122.383 . . 156 99 99 LYS H H 8.019 . . 157 99 99 LYS N N 122.511 . . 158 102 102 THR H H 8.167 . . 159 102 102 THR N N 113.735 . . 160 103 103 SER H H 8.381 . . 161 103 103 SER N N 119.198 . . 162 104 104 ASP H H 8.203 . . 163 104 104 ASP N N 122.272 . . 164 105 105 TYR H H 8.636 . . 165 105 105 TYR N N 116.595 . . 166 106 106 GLY H H 9.253 . . 167 106 106 GLY N N 108.162 . . 168 107 107 PHE H H 8.777 . . 169 107 107 PHE N N 121.007 . . 170 109 109 TYR H H 8.596 . . 171 109 109 TYR N N 117.796 . . 172 110 110 GLY H H 9.008 . . 173 110 110 GLY N N 105.777 . . 174 111 111 ALA H H 8.492 . . 175 111 111 ALA N N 118.846 . . 176 112 112 GLY H H 7.893 . . 177 112 112 GLY N N 105.658 . . 178 113 113 LEU H H 9.009 . . 179 113 113 LEU N N 116.176 . . 180 114 114 GLN H H 7.930 . . 181 114 114 GLN N N 115.313 . . 182 116 116 ASN H H 9.498 . . 183 116 116 ASN N N 119.872 . . 184 118 118 MET H H 7.330 . . 185 118 118 MET N N 109.702 . . 186 119 119 GLU H H 9.090 . . 187 119 119 GLU N N 120.422 . . 188 120 120 ASN H H 8.385 . . 189 120 120 ASN N N 111.509 . . 190 121 121 VAL H H 7.551 . . 191 121 121 VAL N N 117.347 . . 192 122 122 ALA H H 8.209 . . 193 122 122 ALA N N 126.585 . . 194 123 123 LEU H H 9.050 . . 195 123 123 LEU N N 120.129 . . 196 124 124 ASP H H 8.603 . . 197 124 124 ASP N N 126.759 . . 198 125 125 PHE H H 8.705 . . 199 125 125 PHE N N 122.992 . . 200 126 126 SER H H 9.364 . . 201 126 126 SER N N 118.579 . . 202 129 129 GLN H H 9.398 . . 203 129 129 GLN N N 128.676 . . 204 131 131 ARG H H 7.826 . . 205 131 131 ARG N N 126.760 . . 206 132 132 ILE H H 8.799 . . 207 132 132 ILE N N 129.144 . . 208 133 133 ARG H H 9.414 . . 209 133 133 ARG N N 127.114 . . 210 135 135 VAL H H 8.307 . . 211 135 135 VAL N N 124.503 . . 212 136 136 ASP H H 8.001 . . 213 136 136 ASP N N 127.436 . . 214 137 137 VAL H H 8.756 . . 215 137 137 VAL N N 123.910 . . 216 138 138 GLY H H 8.349 . . 217 138 138 GLY N N 116.455 . . 218 139 139 THR H H 8.727 . . 219 139 139 THR N N 124.794 . . 220 141 141 ILE H H 9.099 . . 221 141 141 ILE N N 124.275 . . 222 142 142 ALA H H 8.499 . . 223 142 142 ALA N N 127.355 . . 224 143 143 GLY H H 9.570 . . 225 143 143 GLY N N 108.725 . . 226 144 144 VAL H H 8.868 . . 227 144 144 VAL N N 114.300 . . 228 145 145 GLY H H 8.718 . . 229 145 145 GLY N N 107.482 . . 230 146 146 TYR H H 8.411 . . 231 146 146 TYR N N 121.832 . . 232 147 147 ARG H H 7.621 . . 233 147 147 ARG N N 130.069 . . 234 148 148 PHE H H 8.886 . . 235 148 148 PHE N N 127.839 . . stop_ save_