data_16090 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of a Monomeric Folding Intermediate Reveals the Structural Basis for Rapid Assembly of an Evolutionary Optimized Trimerization Module ; _BMRB_accession_number 16090 _BMRB_flat_file_name bmr16090.str _Entry_type original _Submission_date 2008-12-24 _Accession_date 2008-12-24 _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 Habazettl Judith . . 2 Reiner Andreas . . 3 Kiefhaber Thomas . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 162 "15N chemical shifts" 26 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-02 update BMRB 'edit assembly name' 2009-05-18 update BMRB 'complete entry citation' 2009-04-22 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR Structure of a Monomeric Intermediate on the Evolutionarily Optimized Assembly Pathway of a Small Trimerization Domain' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19361528 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Habazettl Judith . . 2 Reiner Andreas . . 3 Kiefhaber Thomas . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 389 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 103 _Page_last 114 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name foldon_E5R _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label foldon_E5R $foldon_E5R 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_foldon_E5R _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common foldon_E5R _Molecular_mass 3112.573 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; GSGYIPRAPRDGQAYVRKDG EWVLLSTFL ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -1 GLY 2 0 SER 3 1 GLY 4 2 TYR 5 3 ILE 6 4 PRO 7 5 ARG 8 6 ALA 9 7 PRO 10 8 ARG 11 9 ASP 12 10 GLY 13 11 GLN 14 12 ALA 15 13 TYR 16 14 VAL 17 15 ARG 18 16 LYS 19 17 ASP 20 18 GLY 21 19 GLU 22 20 TRP 23 21 VAL 24 22 LEU 25 23 LEU 26 24 SER 27 25 THR 28 26 PHE 29 27 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-05-12 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 2KBL "Nmr Structure Of A Monomeric Folding Intermediate Reveals The Structural Basis For Rapid Assembly Of An Evolutionary Optimized " 100.00 29 100.00 100.00 1.07e-11 stop_ 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 $foldon_E5R 'Enterobacteria phage T4 sensu lato' 348604 Viruses . 'T4-like viruses' 'Enterobacteria phage T4 sensu lato' WAC 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 $foldon_E5R 'recombinant technology' . Escherichia coli 'BL21 (DE3)' pET32A 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 $foldon_E5R 200 uM 'natural abundance' 'K_3 PO_4' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $foldon_E5R 210 uM '[U-99% 15N]' 'K_3 PO_4' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address Bruker . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' 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 'data analysis' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 800 _Details 'TCI, Cryo probe head' 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-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ save_3D_1H-15N_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N TOCSY' _Sample_label $sample_2 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' 10 . mM pH 7.0 . pH pressure 1 . atm temperature 296.7 . 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 H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 water N 15 protons ppm 4.77 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $xwinnmr $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name foldon_E5R _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 4 TYR H H 8.110 0.01 1 2 2 4 TYR HA H 4.599 0.01 1 3 2 4 TYR HB2 H 2.868 0.01 2 4 2 4 TYR HB3 H 2.997 0.01 2 5 2 4 TYR HD1 H 7.062 0.01 3 6 2 4 TYR HD2 H 7.062 0.01 3 7 2 4 TYR HE1 H 6.779 0.01 3 8 2 4 TYR HE2 H 6.779 0.01 3 9 2 4 TYR N N 120.654 0.05 1 10 3 5 ILE H H 8.066 0.01 1 11 3 5 ILE HA H 4.306 0.01 1 12 3 5 ILE HB H 1.694 0.01 1 13 3 5 ILE HD1 H 0.800 0.01 1 14 3 5 ILE HG12 H 1.450 0.01 2 15 3 5 ILE HG13 H 1.057 0.01 2 16 3 5 ILE HG2 H 0.831 0.01 1 17 3 5 ILE N N 127.124 0.05 1 18 4 6 PRO HA H 4.254 0.01 1 19 4 6 PRO HB2 H 2.148 0.01 2 20 4 6 PRO HB3 H 2.254 0.01 2 21 4 6 PRO HD2 H 3.472 0.01 2 22 4 6 PRO HD3 H 3.517 0.01 2 23 4 6 PRO HG2 H 1.864 0.01 2 24 4 6 PRO HG3 H 1.889 0.01 2 25 5 7 ARG H H 8.242 0.01 1 26 5 7 ARG HA H 4.254 0.01 1 27 5 7 ARG HB2 H 1.772 0.01 1 28 5 7 ARG HB3 H 1.694 0.01 1 29 5 7 ARG HD2 H 3.135 0.01 1 30 5 7 ARG HD3 H 3.135 0.01 1 31 5 7 ARG HG2 H 1.626 0.01 1 32 5 7 ARG HG3 H 1.626 0.01 1 33 5 7 ARG N N 120.764 0.05 1 34 6 8 ALA H H 8.241 0.01 1 35 6 8 ALA HA H 4.042 0.01 1 36 6 8 ALA HB H 1.006 0.01 1 37 6 8 ALA N N 126.330 0.05 1 38 7 9 PRO HA H 4.254 0.01 1 39 7 9 PRO HB2 H 2.144 0.01 1 40 7 9 PRO HB3 H 2.144 0.01 1 41 7 9 PRO HD2 H 3.075 0.01 2 42 7 9 PRO HD3 H 3.446 0.01 2 43 7 9 PRO HG2 H 1.770 0.01 2 44 7 9 PRO HG3 H 1.788 0.01 2 45 8 10 ARG H H 8.282 0.01 1 46 8 10 ARG HA H 4.351 0.01 1 47 8 10 ARG HB2 H 1.851 0.01 1 48 8 10 ARG HB3 H 1.680 0.01 1 49 8 10 ARG HD2 H 3.123 0.01 1 50 8 10 ARG HD3 H 3.123 0.01 1 51 8 10 ARG HG2 H 1.572 0.01 1 52 8 10 ARG HG3 H 1.572 0.01 1 53 8 10 ARG N N 120.314 0.05 1 54 9 11 ASP H H 8.197 0.01 1 55 9 11 ASP HA H 4.572 0.01 1 56 9 11 ASP HB2 H 2.769 0.01 1 57 9 11 ASP HB3 H 2.660 0.01 1 58 9 11 ASP N N 120.415 0.05 1 59 10 12 GLY H H 8.492 0.01 1 60 10 12 GLY HA2 H 3.824 0.01 2 61 10 12 GLY HA3 H 4.062 0.01 2 62 10 12 GLY N N 108.979 0.05 1 63 11 13 GLN H H 8.111 0.01 1 64 11 13 GLN HA H 4.454 0.01 1 65 11 13 GLN HB2 H 1.969 0.01 2 66 11 13 GLN HB3 H 1.935 0.01 2 67 11 13 GLN HE21 H 6.830 0.01 2 68 11 13 GLN HE22 H 7.565 0.01 2 69 11 13 GLN HG2 H 2.272 0.01 2 70 11 13 GLN HG3 H 2.189 0.01 2 71 11 13 GLN N N 118.781 0.05 1 72 11 13 GLN NE2 N 112.136 0.05 1 73 12 14 ALA H H 8.282 0.01 1 74 12 14 ALA HA H 4.509 0.01 1 75 12 14 ALA HB H 1.321 0.01 1 76 12 14 ALA N N 123.447 0.05 1 77 13 15 TYR H H 8.383 0.01 1 78 13 15 TYR HA H 5.126 0.01 1 79 13 15 TYR HB2 H 2.994 0.01 1 80 13 15 TYR HB3 H 2.722 0.01 1 81 13 15 TYR HD1 H 6.906 0.01 3 82 13 15 TYR HD2 H 6.906 0.01 3 83 13 15 TYR HE1 H 6.807 0.01 3 84 13 15 TYR HE2 H 6.807 0.01 3 85 13 15 TYR N N 119.333 0.05 1 86 14 16 VAL H H 9.149 0.01 1 87 14 16 VAL HA H 4.618 0.01 1 88 14 16 VAL HB H 2.029 0.01 1 89 14 16 VAL HG1 H 0.897 0.01 2 90 14 16 VAL HG2 H 0.853 0.01 2 91 14 16 VAL N N 118.904 0.05 1 92 15 17 ARG H H 8.471 0.01 1 93 15 17 ARG HA H 4.401 0.01 1 94 15 17 ARG HB2 H 1.499 0.01 1 95 15 17 ARG HB3 H 1.499 0.01 1 96 15 17 ARG HD2 H 2.319 0.01 1 97 15 17 ARG HD3 H 2.319 0.01 1 98 15 17 ARG HG2 H 0.947 0.01 2 99 15 17 ARG HG3 H 0.976 0.01 2 100 15 17 ARG N N 125.066 0.05 1 101 16 18 LYS H H 8.912 0.01 1 102 16 18 LYS HA H 4.395 0.01 1 103 16 18 LYS HB2 H 1.567 0.01 2 104 16 18 LYS HB3 H 1.727 0.01 2 105 16 18 LYS HD2 H 1.599 0.01 1 106 16 18 LYS HD3 H 1.599 0.01 1 107 16 18 LYS HE2 H 2.913 0.01 1 108 16 18 LYS HE3 H 2.913 0.01 1 109 16 18 LYS HG2 H 1.239 0.01 2 110 16 18 LYS HG3 H 1.341 0.01 2 111 16 18 LYS N N 126.761 0.05 1 112 17 19 ASP H H 9.085 0.01 1 113 17 19 ASP HA H 4.287 0.01 1 114 17 19 ASP HB2 H 2.657 0.01 2 115 17 19 ASP HB3 H 2.820 0.01 2 116 17 19 ASP N N 125.647 0.05 1 117 18 20 GLY H H 8.415 0.01 1 118 18 20 GLY HA2 H 3.506 0.01 2 119 18 20 GLY HA3 H 4.017 0.01 2 120 18 20 GLY N N 104.757 0.05 1 121 19 21 GLU H H 7.710 0.01 1 122 19 21 GLU HA H 4.525 0.01 1 123 19 21 GLU HB2 H 2.045 0.01 1 124 19 21 GLU HB3 H 1.829 0.01 1 125 19 21 GLU HG2 H 2.160 0.01 2 126 19 21 GLU HG3 H 2.254 0.01 2 127 19 21 GLU N N 119.170 0.05 1 128 20 22 TRP H H 8.677 0.01 1 129 20 22 TRP HA H 4.989 0.01 1 130 20 22 TRP HB2 H 2.981 0.01 1 131 20 22 TRP HB3 H 3.050 0.01 1 132 20 22 TRP HD1 H 7.172 0.01 1 133 20 22 TRP HE1 H 9.970 0.01 1 134 20 22 TRP HE3 H 7.313 0.01 1 135 20 22 TRP HH2 H 7.182 0.01 1 136 20 22 TRP HZ2 H 7.401 0.01 1 137 20 22 TRP HZ3 H 7.040 0.01 1 138 20 22 TRP N N 122.038 0.05 1 139 20 22 TRP NE1 N 128.660 0.05 1 140 21 23 VAL H H 9.276 0.01 1 141 21 23 VAL HA H 4.548 0.01 1 142 21 23 VAL HB H 2.099 0.01 1 143 21 23 VAL HG1 H 0.941 0.01 1 144 21 23 VAL HG2 H 0.892 0.01 1 145 21 23 VAL N N 122.382 0.05 1 146 22 24 LEU H H 8.486 0.01 1 147 22 24 LEU HA H 4.142 0.01 1 148 22 24 LEU HB2 H 1.461 0.01 1 149 22 24 LEU HB3 H 1.542 0.01 1 150 22 24 LEU HD1 H 0.700 0.01 2 151 22 24 LEU HD2 H 0.580 0.01 2 152 22 24 LEU HG H 1.445 0.01 1 153 22 24 LEU N N 125.477 0.05 1 154 23 25 LEU H H 8.510 0.01 1 155 23 25 LEU HA H 4.321 0.01 1 156 23 25 LEU HB2 H 1.562 0.01 2 157 23 25 LEU HB3 H 1.598 0.01 2 158 23 25 LEU HD1 H 0.879 0.01 2 159 23 25 LEU HD2 H 0.848 0.01 2 160 23 25 LEU HG H 1.478 0.01 1 161 23 25 LEU N N 125.983 0.05 1 162 24 26 SER H H 8.316 0.01 1 163 24 26 SER HA H 4.419 0.01 1 164 24 26 SER HB2 H 3.761 0.01 1 165 24 26 SER HB3 H 3.861 0.01 1 166 24 26 SER N N 115.544 0.05 1 167 25 27 THR H H 7.884 0.01 1 168 25 27 THR HA H 4.252 0.01 1 169 25 27 THR HB H 4.106 0.01 1 170 25 27 THR HG2 H 1.095 0.01 1 171 25 27 THR N N 114.664 0.05 1 172 26 28 PHE H H 8.069 0.01 1 173 26 28 PHE HA H 4.657 0.01 1 174 26 28 PHE HB2 H 3.218 0.01 1 175 26 28 PHE HB3 H 2.968 0.01 1 176 26 28 PHE HD1 H 7.259 0.01 3 177 26 28 PHE HD2 H 7.259 0.01 3 178 26 28 PHE HE1 H 7.301 0.01 3 179 26 28 PHE HE2 H 7.301 0.01 3 180 26 28 PHE HZ H 7.265 0.01 1 181 26 28 PHE N N 121.669 0.05 1 182 27 29 LEU H H 7.687 0.01 1 183 27 29 LEU HA H 4.173 0.01 1 184 27 29 LEU HB2 H 1.559 0.01 1 185 27 29 LEU HB3 H 1.559 0.01 1 186 27 29 LEU HD1 H 0.855 0.01 2 187 27 29 LEU HD2 H 0.855 0.01 2 188 27 29 LEU N N 128.522 0.05 1 stop_ save_