data_50085 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Collective exchange processes reveal an active site proton cage in bacteriorhodopsin ; _BMRB_accession_number 50085 _BMRB_flat_file_name bmr50085.str _Entry_type original _Submission_date 2019-11-11 _Accession_date 2019-11-11 _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 Friedrich Daniel . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 44 "13C chemical shifts" 2 "15N chemical shifts" 42 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-03-12 update BMRB 'update entry citation' 2020-01-06 original author 'original release' stop_ _Original_release_date 2019-11-12 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Collective exchange processes reveal an active site proton cage in bacteriorhodopsin ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31925324 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Friedrich Daniel . . 2 Brunig Florian N. . 3 Nieuwkoop Andrew J. . 4 Netz Roland R. . 5 Hegemann Peter . . 6 Oschkinat Hartmut . . stop_ _Journal_abbreviation 'Commun. Biol.' _Journal_volume 3 _Journal_issue 1 _Journal_ISSN 2399-3642 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4 _Page_last 4 _Year 2020 _Details . save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name bacteriorhodopsin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label bacteriorhodopsin $entity_1 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 248 _Mol_residue_sequence ; QAQITGRPEWIWLALGTALM GLGTLYFLVKGMGVSDPDAK KFYAITTLVPAIAFTMYLSM LLGYGLTMVPFGGEQNPIYW ARYADWLFTTPLLLLDLALL VDADQGTILALVGADGIMIG TGLVGALTKVYSYRFVWWAI STAAMLYILYVLFFGFTSLA ESMRPEVASTFKVLRNVTVV LWSAYPVVWLIGSEGAGIVP LNIETLLFMVLDVSAKVGFG LILLRSRAIFGEAEAPEPSA GDGAAATS ; loop_ _Residue_seq_code _Residue_label 1 GLN 2 ALA 3 GLN 4 ILE 5 THR 6 GLY 7 ARG 8 PRO 9 GLU 10 TRP 11 ILE 12 TRP 13 LEU 14 ALA 15 LEU 16 GLY 17 THR 18 ALA 19 LEU 20 MET 21 GLY 22 LEU 23 GLY 24 THR 25 LEU 26 TYR 27 PHE 28 LEU 29 VAL 30 LYS 31 GLY 32 MET 33 GLY 34 VAL 35 SER 36 ASP 37 PRO 38 ASP 39 ALA 40 LYS 41 LYS 42 PHE 43 TYR 44 ALA 45 ILE 46 THR 47 THR 48 LEU 49 VAL 50 PRO 51 ALA 52 ILE 53 ALA 54 PHE 55 THR 56 MET 57 TYR 58 LEU 59 SER 60 MET 61 LEU 62 LEU 63 GLY 64 TYR 65 GLY 66 LEU 67 THR 68 MET 69 VAL 70 PRO 71 PHE 72 GLY 73 GLY 74 GLU 75 GLN 76 ASN 77 PRO 78 ILE 79 TYR 80 TRP 81 ALA 82 ARG 83 TYR 84 ALA 85 ASP 86 TRP 87 LEU 88 PHE 89 THR 90 THR 91 PRO 92 LEU 93 LEU 94 LEU 95 LEU 96 ASP 97 LEU 98 ALA 99 LEU 100 LEU 101 VAL 102 ASP 103 ALA 104 ASP 105 GLN 106 GLY 107 THR 108 ILE 109 LEU 110 ALA 111 LEU 112 VAL 113 GLY 114 ALA 115 ASP 116 GLY 117 ILE 118 MET 119 ILE 120 GLY 121 THR 122 GLY 123 LEU 124 VAL 125 GLY 126 ALA 127 LEU 128 THR 129 LYS 130 VAL 131 TYR 132 SER 133 TYR 134 ARG 135 PHE 136 VAL 137 TRP 138 TRP 139 ALA 140 ILE 141 SER 142 THR 143 ALA 144 ALA 145 MET 146 LEU 147 TYR 148 ILE 149 LEU 150 TYR 151 VAL 152 LEU 153 PHE 154 PHE 155 GLY 156 PHE 157 THR 158 SER 159 LEU 160 ALA 161 GLU 162 SER 163 MET 164 ARG 165 PRO 166 GLU 167 VAL 168 ALA 169 SER 170 THR 171 PHE 172 LYS 173 VAL 174 LEU 175 ARG 176 ASN 177 VAL 178 THR 179 VAL 180 VAL 181 LEU 182 TRP 183 SER 184 ALA 185 TYR 186 PRO 187 VAL 188 VAL 189 TRP 190 LEU 191 ILE 192 GLY 193 SER 194 GLU 195 GLY 196 ALA 197 GLY 198 ILE 199 VAL 200 PRO 201 LEU 202 ASN 203 ILE 204 GLU 205 THR 206 LEU 207 LEU 208 PHE 209 MET 210 VAL 211 LEU 212 ASP 213 VAL 214 SER 215 ALA 216 LYS 217 VAL 218 GLY 219 PHE 220 GLY 221 LEU 222 ILE 223 LEU 224 LEU 225 ARG 226 SER 227 ARG 228 ALA 229 ILE 230 PHE 231 GLY 232 GLU 233 ALA 234 GLU 235 ALA 236 PRO 237 GLU 238 PRO 239 SER 240 ALA 241 GLY 242 ASP 243 GLY 244 ALA 245 ALA 246 ALA 247 THR 248 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source_1 _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 'Halobacterium salinarum' 2242 Archaea . Halobacterium salinarum stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $entity_1 'native organism' . Halobacterium salinarum . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solid-state _Details 'purple membranes' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 10 mM DCN stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CcpNMR . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details ; The CCPN data model for NMR spectroscopy: development of a software pipeline. Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED. Proteins. 2005 Jun 1;59(4):687-96. ; save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _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_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'purple membranes' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.5 . pH temperature 290 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 na indirect . . . . DSS H 1 'methyl protons' ppm 0 internal direct . . . 1 DSS N 15 'methyl protons' ppm 0 na indirect . . . . 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details ; RSB (BR555), 13.22, 173.51 RSB (BR568), 12.24, 165.42 13.22 ppm is the 1H chemical shift of the retinal Schiff base proton in the BR555 state (13-cis,15-syn retinal configuration) of bacteriorhodopsin. 173.51 ppm is the 15N chemical shift of the retinal Schiff base nitrogen in the BR555 state (13-cis,15-syn retinal configuration) of bacteriorhodopsin. 12.24 ppm is the 1H chemical shift of the retinal Schiff base proton in the BR568 state (13-trans,15-anti retinal configuration) of bacteriorhodopsin. 165.42 ppm is the 15N chemical shift of the retinal Schiff base nitrogen in the BR568 state (13-trans,15-anti retinal configuration) of bacteriorhodopsin. ; loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name bacteriorhodopsin _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 39 39 ALA H H 8.03 . 1 2 39 39 ALA N N 123.75 . 1 3 40 40 LYS H H 8.52 . 1 4 40 40 LYS N N 116.11 . 1 5 41 41 LYS H H 7.29 . 1 6 41 41 LYS N N 117.73 . 1 7 42 42 PHE H H 7.15 . 1 8 42 42 PHE N N 115.03 . 1 9 43 43 TYR H H 8.88 . 1 10 43 43 TYR N N 120.67 . 1 11 44 44 ALA H H 8.18 . 1 12 44 44 ALA N N 123.61 . 1 13 45 45 ILE H H 7.76 . 1 14 45 45 ILE N N 114.42 . 1 15 71 71 PHE H H 7.58 . 1 16 71 71 PHE N N 114.01 . 1 17 72 72 GLY H H 9.52 . 1 18 72 72 GLY N N 109.69 . 1 19 73 73 GLY H H 8.55 . 1 20 73 73 GLY N N 105.85 . 1 21 74 74 GLU H H 7.15 . 1 22 74 74 GLU N N 117.72 . 1 23 75 75 GLN H H 8.43 . 1 24 75 75 GLN N N 118.83 . 1 25 76 76 ASN H H 7.78 . 1 26 76 76 ASN N N 122.48 . 1 27 78 78 ILE H H 8.75 . 1 28 78 78 ILE N N 125.88 . 1 29 79 79 TYR H H 8.45 . 1 30 79 79 TYR N N 127.51 . 1 31 80 80 TRP H H 7.32 . 1 32 80 80 TRP N N 125.03 . 1 33 81 81 ALA H H 6.26 . 1 34 81 81 ALA N N 124.23 . 1 35 82 82 ARG HE H 6.24 . 1 36 82 82 ARG NE N 77.65 . 1 37 85 85 ASP HD2 H 12.12 . 1 38 85 85 ASP CG C 169.68 . 1 39 96 96 ASP HD2 H 11.04 . 1 40 96 96 ASP CG C 170.78 . 1 41 106 106 GLY H H 8.93 . 1 42 106 106 GLY N N 104.83 . 1 43 107 107 THR H H 7.34 . 1 44 107 107 THR N N 118.08 . 1 45 108 108 ILE H H 7.7 . 1 46 108 108 ILE N N 119.36 . 1 47 109 109 LEU H H 8.05 . 1 48 109 109 LEU N N 118.66 . 1 49 110 110 ALA H H 7.71 . 1 50 110 110 ALA N N 118.65 . 1 51 128 128 THR H H 7.3 . 1 52 128 128 THR N N 118.23 . 1 53 129 129 LYS H H 8.84 . 1 54 129 129 LYS N N 118.8 . 1 55 130 130 VAL H H 7.75 . 1 56 130 130 VAL N N 117.19 . 1 57 131 131 TYR H H 8.74 . 1 58 131 131 TYR N N 128.38 . 1 59 132 132 SER H H 8.7 . 1 60 132 132 SER N N 109.94 . 1 61 166 166 GLU H H 9.75 . 1 62 166 166 GLU N N 116.24 . 1 63 167 167 VAL H H 7.3 . 1 64 167 167 VAL N N 120.5 . 1 65 168 168 ALA H H 7.65 . 1 66 168 168 ALA N N 121.12 . 1 67 169 169 SER H H 8.36 . 1 68 169 169 SER N N 110.87 . 1 69 170 170 THR H H 7.23 . 1 70 170 170 THR N N 118.66 . 1 71 195 195 GLY H H 6.67 . 1 72 195 195 GLY N N 105.91 . 1 73 196 196 ALA H H 9.53 . 1 74 196 196 ALA N N 129.23 . 1 75 197 197 GLY H H 8.28 . 1 76 197 197 GLY N N 106.46 . 1 77 203 203 ILE H H 6.73 . 1 78 203 203 ILE N N 118.98 . 1 79 204 204 GLU H H 8.59 . 1 80 204 204 GLU N N 120.94 . 1 81 205 205 THR H H 8.31 . 1 82 205 205 THR N N 113.2 . 1 83 206 206 LEU H H 7.07 . 1 84 206 206 LEU N N 126.45 . 1 85 207 207 LEU H H 7.55 . 1 86 207 207 LEU N N 121.23 . 1 87 208 208 PHE H H 9.23 . 1 88 208 208 PHE N N 125.72 . 1 stop_ save_