data_15612 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Extended Polypeptide Linkers Establish the Spatial Architecture of a Pyruvate Dehydrogenase ; _BMRB_accession_number 15612 _BMRB_flat_file_name bmr15612.str _Entry_type new _Submission_date 2008-01-02 _Accession_date 2008-01-02 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Milne Jacqueline L.S. . 2 Stott Katherine M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 144 "13C chemical shifts" 72 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-26 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex ; _Citation_status published _Citation_type journal _PubMed_ID 18184587 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lengyel Jeffrey S. . 2 Stott Katherine M. . 3 Wu Xiongwu . . 4 Brooks Bernard R. . 5 Balbo Andrea . . 6 Schuck Peter . . 7 Perham Richard N. . 8 Subramaniam Sriram . . 9 Milne Jacqueline L.S. . stop_ _Journal_abbreviation Structure _Journal_volume 16 _Journal_issue 1 _Page_first 93 _Page_last 103 _Year 2008 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Inner-linker peptide from PDH' loop_ _Mol_system_component_name _Mol_label 'Inner-linker peptide' $Inner-linker_peptide stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_Inner-linker_peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Inner-linker_peptide _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 37 _Mol_residue_sequence ; AGGAKPAPAAAEEKAAPAAA KPATTEGEFPETREKMS ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 GLY 3 GLY 4 ALA 5 LYS 6 PRO 7 ALA 8 PRO 9 ALA 10 ALA 11 ALA 12 GLU 13 GLU 14 LYS 15 ALA 16 ALA 17 PRO 18 ALA 19 ALA 20 ALA 21 LYS 22 PRO 23 ALA 24 THR 25 THR 26 GLU 27 GLY 28 GLU 29 PHE 30 PRO 31 GLU 32 THR 33 ARG 34 GLU 35 LYS 36 MET 37 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-05 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 1B5S "Dihydrolipoyl Transacetylase (e.c.2.3.1.12) Catalytic Domain (residues 184-425) From Bacillus Stearothermophilus" 54.05 242 100.00 100.00 8.56e-03 PDB 3DUF "Snapshots Of Catalysis In The E1 Subunit Of The Pyruvate Dehydrogenase Multi-Enzyme Complex" 100.00 428 100.00 100.00 2.98e-12 PDB 3DV0 "Snapshots Of Catalysis In The E1 Subunit Of The Pyruvate Dehydrogenase Multi-Enzyme Complex" 100.00 428 100.00 100.00 2.98e-12 PDB 3DVA "Snapshots Of Catalysis In The E1 Subunit Of The Pyruvate Dehydrogenase Multi-Enzyme Complex" 100.00 428 100.00 100.00 2.98e-12 EMBL CAA37630 "dihydrolipoamide acetyltransferase [Geobacillus stearothermophilus]" 100.00 428 100.00 100.00 2.98e-12 GB KFL17224 "branched-chain alpha-keto acid dehydrogenase subunit E2 [Geobacillus stearothermophilus]" 100.00 428 97.30 97.30 2.03e-11 GB KFX35197 "branched-chain alpha-keto acid dehydrogenase subunit E2 [Geobacillus stearothermophilus]" 100.00 428 97.30 97.30 2.03e-11 GB KMY60230 "branched-chain alpha-keto acid dehydrogenase subunit E2 [Geobacillus stearothermophilus]" 100.00 428 100.00 100.00 2.98e-12 GB KMY60559 "branched-chain alpha-keto acid dehydrogenase subunit E2 [Geobacillus stearothermophilus]" 100.00 428 100.00 100.00 2.98e-12 GB KMY62515 "branched-chain alpha-keto acid dehydrogenase subunit E2 [Geobacillus stearothermophilus]" 100.00 428 100.00 100.00 2.98e-12 REF WP_033008489 "branched-chain alpha-keto acid dehydrogenase subunit E2 [Geobacillus stearothermophilus]" 100.00 428 97.30 97.30 2.03e-11 REF WP_033016211 "MULTISPECIES: dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex [Geobacillus]" 100.00 428 100.00 100.00 2.98e-12 SP P11961 "RecName: Full=Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex; AltName: Full=Dihydrol" 100.00 428 100.00 100.00 2.98e-12 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Inner-linker_peptide 'Bacillus stearothermophilus' 1422 Bacteria . Bacillus stearothermophilus 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 $Inner-linker_peptide 'chemical synthesis' . . . . ? stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Inner-linker_peptide 1 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' DSS 0.01 mM 'natural abundance' D2O 10 % '[U-100% 2H]' H2O 90 % . stop_ save_ ############################ # Computer software used # ############################ save_CCPNMR _Saveframe_category software _Name CCPNMR loop_ _Vendor _Address _Electronic_address 'Wayne Boucher and Tim Stevens' . . stop_ loop_ _Task 'chemical shift assignment' stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_3 _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 loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 0.01 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference 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 0.00 internal direct ? ? ? 1.000000 DSS C 13 'methyl protons' ppm 0.00 internal indirect ? ? ? 0.251449530 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 loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C 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 'Inner-linker peptide' 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 GLY H H 8.726 0.000 1 2 2 2 GLY HA2 H 4.048 0.001 1 3 2 2 GLY HA3 H 4.048 0.001 1 4 2 2 GLY CA C 45.459 0.000 1 5 3 3 GLY H H 8.402 0.000 1 6 3 3 GLY HA2 H 3.982 0.000 1 7 3 3 GLY HA3 H 3.982 0.000 1 8 3 3 GLY CA C 45.189 0.000 1 9 4 4 ALA H H 8.222 0.000 1 10 4 4 ALA HA H 4.330 0.000 1 11 4 4 ALA HB H 1.376 0.000 1 12 4 4 ALA CA C 52.451 0.000 1 13 4 4 ALA CB C 19.541 0.000 1 14 5 5 LYS H H 8.392 0.001 1 15 5 5 LYS HA H 4.608 0.002 1 16 5 5 LYS HB2 H 1.731 0.002 2 17 5 5 LYS HB3 H 1.828 0.003 2 18 5 5 LYS HD2 H 1.723 0.006 1 19 5 5 LYS HD3 H 1.723 0.006 1 20 5 5 LYS HE2 H 3.017 0.001 1 21 5 5 LYS HE3 H 3.017 0.001 1 22 5 5 LYS HG2 H 1.491 0.003 1 23 5 5 LYS HG3 H 1.491 0.003 1 24 5 5 LYS CA C 54.271 0.000 1 25 5 5 LYS CB C 32.793 0.001 1 26 5 5 LYS CD C 29.365 0.000 1 27 5 5 LYS CE C 42.358 0.000 1 28 5 5 LYS CG C 24.746 0.000 1 29 6 6 PRO HA H 4.412 0.000 1 30 7 7 ALA H H 8.438 0.002 1 31 7 7 ALA HA H 4.590 0.000 1 32 7 7 ALA HB H 1.378 0.002 1 33 7 7 ALA CA C 50.661 0.000 1 34 7 7 ALA CB C 18.246 0.000 1 35 12 12 GLU H H 8.401 0.001 1 36 12 12 GLU HA H 4.285 0.000 1 37 12 12 GLU HB2 H 1.972 0.000 2 38 12 12 GLU HB3 H 2.051 0.000 2 39 12 12 GLU HG2 H 2.303 0.000 1 40 12 12 GLU HG3 H 2.303 0.000 1 41 12 12 GLU CA C 56.694 0.000 1 42 12 12 GLU CB C 30.256 0.001 1 43 12 12 GLU CG C 35.969 0.000 1 44 13 13 GLU H H 8.345 0.000 1 45 13 13 GLU HA H 4.275 0.000 1 46 13 13 GLU HB2 H 1.966 0.000 2 47 13 13 GLU HB3 H 2.065 0.000 2 48 13 13 GLU HG2 H 2.295 0.000 1 49 13 13 GLU HG3 H 2.295 0.000 1 50 13 13 GLU CA C 56.700 0.000 1 51 13 13 GLU CB C 30.251 0.003 1 52 13 13 GLU CG C 35.973 0.000 1 53 16 16 ALA H H 8.317 0.000 1 54 16 16 ALA HA H 4.590 0.000 1 55 16 16 ALA HB H 1.374 0.002 1 56 16 16 ALA CA C 50.661 0.000 1 57 16 16 ALA CB C 18.246 0.000 1 58 21 21 LYS H H 8.303 0.001 1 59 21 21 LYS HA H 4.608 0.002 1 60 21 21 LYS HB2 H 1.731 0.002 2 61 21 21 LYS HB3 H 1.829 0.003 2 62 21 21 LYS HD2 H 1.723 0.006 1 63 21 21 LYS HD3 H 1.723 0.006 1 64 21 21 LYS HE2 H 3.017 0.001 1 65 21 21 LYS HE3 H 3.017 0.001 1 66 21 21 LYS HG2 H 1.489 0.000 1 67 21 21 LYS HG3 H 1.489 0.000 1 68 21 21 LYS CA C 54.271 0.000 1 69 21 21 LYS CB C 32.793 0.001 1 70 21 21 LYS CD C 29.365 0.000 1 71 21 21 LYS CE C 42.358 0.000 1 72 21 21 LYS CG C 24.746 0.000 1 73 22 22 PRO HA H 4.426 0.000 1 74 22 22 PRO HB2 H 2.326 0.000 1 75 22 22 PRO HB3 H 2.326 0.000 1 76 22 22 PRO HG2 H 1.940 0.000 1 77 22 22 PRO HG3 H 1.940 0.000 1 78 22 22 PRO CA C 63.196 0.000 1 79 22 22 PRO CB C 32.273 0.000 1 80 22 22 PRO CG C 27.575 0.000 1 81 23 23 ALA H H 8.524 0.002 1 82 23 23 ALA HA H 4.380 0.001 1 83 23 23 ALA HB H 1.433 0.000 1 84 23 23 ALA CA C 52.743 0.000 1 85 23 23 ALA CB C 19.455 0.000 1 86 24 24 THR H H 8.176 0.003 1 87 24 24 THR HA H 4.459 0.001 1 88 24 24 THR HB H 4.283 0.001 1 89 24 24 THR HG1 H 5.151 0.000 1 90 24 24 THR HG2 H 1.223 0.001 1 91 24 24 THR CA C 61.690 0.000 1 92 24 24 THR CB C 70.104 0.000 1 93 24 24 THR CG2 C 21.782 0.000 1 94 25 25 THR H H 8.227 0.002 1 95 25 25 THR HA H 4.391 0.002 1 96 25 25 THR HB H 4.266 0.001 1 97 25 25 THR HG1 H 5.213 0.000 1 98 25 25 THR HG2 H 1.209 0.001 1 99 25 25 THR CA C 62.015 0.000 1 100 25 25 THR CB C 69.985 0.000 1 101 25 25 THR CG2 C 21.735 0.000 1 102 26 26 GLU H H 8.476 0.002 1 103 26 26 GLU HA H 4.263 0.001 1 104 26 26 GLU HB2 H 1.966 0.000 2 105 26 26 GLU HB3 H 2.060 0.000 2 106 26 26 GLU HG2 H 2.324 0.000 1 107 26 26 GLU HG3 H 2.324 0.000 1 108 26 26 GLU CA C 56.736 0.000 1 109 26 26 GLU CB C 30.285 0.005 1 110 26 26 GLU CG C 35.957 0.000 1 111 27 27 GLY H H 8.405 0.003 1 112 27 27 GLY HA2 H 3.905 0.001 2 113 27 27 GLY HA3 H 3.933 0.000 2 114 27 27 GLY CA C 45.335 0.003 1 115 28 28 GLU H H 8.058 0.002 1 116 28 28 GLU HA H 4.206 0.002 1 117 28 28 GLU HB2 H 1.833 0.007 2 118 28 28 GLU HB3 H 1.864 0.009 2 119 28 28 GLU HG2 H 2.044 0.009 2 120 28 28 GLU HG3 H 2.176 0.003 2 121 28 28 GLU CA C 56.483 0.000 1 122 28 28 GLU CB C 30.445 0.000 1 123 28 28 GLU CG C 35.584 0.000 1 124 29 29 PHE H H 8.343 0.003 1 125 29 29 PHE HA H 4.929 0.002 1 126 29 29 PHE HB2 H 2.932 0.005 2 127 29 29 PHE HB3 H 3.205 0.005 2 128 29 29 PHE HD1 H 7.315 0.003 3 129 29 29 PHE HD2 H 7.315 0.003 3 130 29 29 PHE HE1 H 7.346 0.000 3 131 29 29 PHE HE2 H 7.346 0.000 3 132 29 29 PHE HZ H 7.310 0.000 1 133 29 29 PHE CB C 39.317 0.006 1 134 29 29 PHE CD1 C 132.325 0.000 3 135 29 29 PHE CD2 C 132.325 0.000 3 136 29 29 PHE CE1 C 131.561 0.000 3 137 29 29 PHE CE2 C 131.561 0.000 3 138 29 29 PHE CZ C 130.018 0.000 1 139 30 30 PRO HA H 4.443 0.002 1 140 30 30 PRO HB2 H 2.305 0.002 1 141 30 30 PRO HB3 H 2.305 0.002 1 142 30 30 PRO HD2 H 3.633 0.007 2 143 30 30 PRO HD3 H 3.781 0.002 2 144 30 30 PRO HG2 H 1.985 0.039 1 145 30 30 PRO CA C 63.642 0.000 1 146 30 30 PRO CB C 32.267 0.000 1 147 30 30 PRO CD C 50.829 0.002 1 148 30 30 PRO CG C 27.596 0.002 1 149 31 31 GLU H H 8.624 0.003 1 150 31 31 GLU HA H 4.358 0.003 1 151 31 31 GLU HB2 H 2.027 0.003 2 152 31 31 GLU HB3 H 2.097 0.006 2 153 31 31 GLU HG2 H 2.362 0.001 1 154 31 31 GLU HG3 H 2.362 0.001 1 155 31 31 GLU CA C 56.989 0.000 1 156 31 31 GLU CB C 30.239 0.000 1 157 31 31 GLU CG C 35.973 0.000 1 158 32 32 THR H H 8.217 0.003 1 159 32 32 THR HA H 4.357 0.002 1 160 32 32 THR HB H 4.266 0.000 1 161 32 32 THR HG1 H 5.258 0.000 1 162 32 32 THR HG2 H 1.236 0.001 1 163 32 32 THR CA C 62.179 0.000 1 164 32 32 THR CB C 69.985 0.000 1 165 32 32 THR CG2 C 21.855 0.000 1 166 33 33 ARG H H 8.347 0.001 1 167 33 33 ARG HA H 4.377 0.000 1 168 33 33 ARG HB2 H 1.791 0.001 2 169 33 33 ARG HB3 H 1.887 0.002 2 170 33 33 ARG HD2 H 3.206 0.000 1 171 33 33 ARG HD3 H 3.206 0.000 1 172 33 33 ARG HE H 7.256 0.002 1 173 33 33 ARG HG2 H 1.653 0.002 1 174 33 33 ARG HG3 H 1.653 0.002 1 175 33 33 ARG CB C 31.085 0.002 1 176 33 33 ARG CD C 43.538 0.000 1 177 33 33 ARG CG C 27.253 0.000 1 178 34 34 GLU H H 8.449 0.002 1 179 34 34 GLU HA H 4.267 0.000 1 180 34 34 GLU HB2 H 1.963 0.000 2 181 34 34 GLU HB3 H 2.065 0.000 2 182 34 34 GLU HG2 H 2.319 0.000 1 183 34 34 GLU HG3 H 2.319 0.000 1 184 34 34 GLU CB C 30.249 0.003 1 185 34 34 GLU CG C 35.897 0.000 1 186 35 35 LYS H H 8.355 0.001 1 187 35 35 LYS HA H 4.328 0.000 1 188 35 35 LYS HB2 H 1.774 0.000 2 189 35 35 LYS HB3 H 1.859 0.000 2 190 35 35 LYS HD2 H 1.696 0.000 1 191 35 35 LYS HD3 H 1.696 0.000 1 192 35 35 LYS HE2 H 3.013 0.000 1 193 35 35 LYS HE3 H 3.013 0.000 1 194 35 35 LYS HG2 H 1.452 0.001 1 195 35 35 LYS HG3 H 1.452 0.001 1 196 35 35 LYS CB C 33.266 0.003 1 197 35 35 LYS CD C 29.291 0.000 1 198 35 35 LYS CG C 24.882 0.000 1 199 36 36 MET H H 8.486 0.002 1 200 36 36 MET HA H 4.559 0.004 1 201 36 36 MET HB2 H 2.029 0.002 2 202 36 36 MET HB3 H 2.181 0.002 2 203 36 36 MET HE H 2.114 0.000 1 204 36 36 MET HG2 H 2.569 0.002 2 205 36 36 MET HG3 H 2.653 0.000 2 206 36 36 MET CA C 55.716 0.000 1 207 36 36 MET CB C 33.242 0.000 1 208 36 36 MET CE C 17.139 0.000 1 209 36 36 MET CG C 32.283 0.000 1 210 37 37 SER H H 7.962 0.002 1 211 37 37 SER HA H 4.276 0.001 1 212 37 37 SER HB2 H 3.867 0.001 1 213 37 37 SER HB3 H 3.867 0.001 1 214 37 37 SER HG H 5.742 0.000 1 215 37 37 SER CA C 60.142 0.000 1 216 37 37 SER CB C 64.998 0.000 1 stop_ save_