data_11524 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of designed protein, AF.2A1, (Ensembles) ; _BMRB_accession_number 11524 _BMRB_flat_file_name bmr11524.str _Entry_type original _Submission_date 2013-04-18 _Accession_date 2013-04-18 _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 Watanabe Hideki . . 2 Yamasaki Kazuhiko . . 3 Honda Shinya . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 137 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-01-02 original author . stop_ _Original_release_date 2014-01-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structurally guided stepwise segment elongation for the design of a small sized protein: implications for primordial protein evolution' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24356963 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Watanabe Hideki . . 2 Yamasaki Kazuhiko . . 3 Honda Shinya . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name AF.2A1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $entity 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2716.968 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; GVVRQWSGYDPRTGTWRSSI AYGGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 VAL 3 3 VAL 4 4 ARG 5 5 GLN 6 6 TRP 7 7 SER 8 8 GLY 9 9 TYR 10 10 ASP 11 11 PRO 12 12 ARG 13 13 THR 14 14 GLY 15 15 THR 16 16 TRP 17 17 ARG 18 18 SER 19 19 SER 20 20 ILE 21 21 ALA 22 22 TYR 23 23 GLY 24 24 GLY 25 25 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-10 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 2RT4 "Nmr Structure Of Designed Protein, Af.2a1, (ensembles)" 100.00 25 100.00 100.00 1.56e-07 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity . . . . . . 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 'chemical synthesis' . . . . . 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 $entity 1.8 mM 'natural abundance' 'sodium acetate-d4' 10 mM '[U-100% 2H]' D2O 5 % . H2O 95 % . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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' 10 . mM pH 4.5 . pH pressure 1 . atm temperature 283 . 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 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 '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D DQF-COSY' 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 entity _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 1 1 GLY HA2 H 3.875 0.002 1 2 1 1 GLY HA3 H 3.875 0.002 1 3 2 2 VAL H H 8.563 0.001 1 4 2 2 VAL HA H 4.189 0.004 1 5 2 2 VAL HB H 2.035 0.002 1 6 2 2 VAL HG1 H 0.923 0.006 1 7 2 2 VAL HG2 H 0.923 0.006 1 8 3 3 VAL H H 8.521 0.002 1 9 3 3 VAL HA H 4.096 0.001 1 10 3 3 VAL HB H 2.002 0 1 11 3 3 VAL HG1 H 0.894 0.002 2 12 3 3 VAL HG2 H 0.942 0.005 2 13 4 4 ARG H H 8.596 0.005 1 14 4 4 ARG HA H 4.284 0.001 1 15 4 4 ARG HB2 H 1.648 0.003 1 16 4 4 ARG HB3 H 1.648 0.003 1 17 4 4 ARG HG2 H 1.506 0.004 2 18 4 4 ARG HG3 H 1.429 0.007 2 19 4 4 ARG HD2 H 3.006 0.003 1 20 4 4 ARG HD3 H 3.006 0.003 1 21 4 4 ARG HE H 7.063 0.005 1 22 5 5 GLN H H 8.510 0.003 1 23 5 5 GLN HA H 4.378 0.004 1 24 5 5 GLN HB2 H 1.992 0.003 2 25 5 5 GLN HB3 H 1.899 0.011 2 26 5 5 GLN HG2 H 2.258 0.004 1 27 5 5 GLN HG3 H 2.258 0.004 1 28 6 6 TRP H H 8.524 0.002 1 29 6 6 TRP HA H 4.732 0.001 1 30 6 6 TRP HB2 H 3.249 0.005 2 31 6 6 TRP HB3 H 3.184 0.006 2 32 6 6 TRP HD1 H 7.189 0.003 1 33 6 6 TRP HE1 H 10.110 0.003 1 34 6 6 TRP HE3 H 7.438 0.004 1 35 6 6 TRP HZ2 H 7.386 0 1 36 6 6 TRP HZ3 H 6.960 0.003 1 37 6 6 TRP HH2 H 7.119 0 1 38 7 7 SER H H 8.303 0.004 1 39 7 7 SER HA H 4.480 0.004 1 40 7 7 SER HB2 H 3.787 0.003 1 41 7 7 SER HB3 H 3.787 0.003 1 42 8 8 GLY H H 7.882 0.003 1 43 8 8 GLY HA2 H 3.816 0.004 2 44 8 8 GLY HA3 H 3.662 0.004 2 45 9 9 TYR H H 8.126 0.003 1 46 9 9 TYR HA H 4.164 0.004 1 47 9 9 TYR HB2 H 2.544 0.003 2 48 9 9 TYR HB3 H 2.233 0.004 2 49 9 9 TYR HD1 H 6.463 0.004 1 50 9 9 TYR HD2 H 6.463 0.004 1 51 9 9 TYR HE1 H 6.574 0.005 1 52 9 9 TYR HE2 H 6.574 0.005 1 53 10 10 ASP H H 8.232 0.003 1 54 10 10 ASP HA H 4.856 0.003 1 55 10 10 ASP HB2 H 2.937 0.003 2 56 10 10 ASP HB3 H 2.360 0 2 57 11 11 PRO HA H 4.141 0.002 1 58 11 11 PRO HB2 H 2.336 0.003 1 59 11 11 PRO HB3 H 2.372 0.001 1 60 11 11 PRO HG2 H 1.985 0.003 1 61 11 11 PRO HG3 H 1.985 0.003 1 62 11 11 PRO HD2 H 3.807 0.005 1 63 11 11 PRO HD3 H 3.721 0.005 1 64 12 12 ARG H H 8.188 0.003 1 65 12 12 ARG HA H 4.150 0.001 1 66 12 12 ARG HB2 H 1.879 0.002 1 67 12 12 ARG HB3 H 1.879 0.002 1 68 12 12 ARG HG2 H 1.621 0.005 2 69 12 12 ARG HG3 H 1.567 0.004 2 70 12 12 ARG HD2 H 3.162 0.001 1 71 12 12 ARG HD3 H 3.162 0.001 1 72 12 12 ARG HE H 7.435 0.002 1 73 13 13 THR H H 7.381 0.005 1 74 13 13 THR HA H 4.374 0.003 1 75 13 13 THR HB H 4.290 0.002 1 76 13 13 THR HG2 H 1.132 0.005 1 77 14 14 GLY H H 8.408 0.002 1 78 14 14 GLY HA2 H 4.019 0.003 2 79 14 14 GLY HA3 H 3.837 0.005 2 80 15 15 THR H H 7.575 0.004 1 81 15 15 THR HA H 4.542 0.003 1 82 15 15 THR HB H 4.194 0.002 1 83 15 15 THR HG2 H 1.162 0.004 1 84 16 16 TRP H H 8.647 0.004 1 85 16 16 TRP HA H 4.667 0.002 1 86 16 16 TRP HB2 H 3.234 0.008 2 87 16 16 TRP HB3 H 3.117 0.006 2 88 16 16 TRP HD1 H 7.217 0.003 1 89 16 16 TRP HE1 H 10.178 0.002 1 90 16 16 TRP HE3 H 7.425 0.002 1 91 16 16 TRP HZ2 H 7.307 0.002 1 92 16 16 TRP HZ3 H 7.086 0.007 1 93 16 16 TRP HH2 H 7.110 0 1 94 17 17 ARG H H 8.362 0.003 1 95 17 17 ARG HA H 4.353 0.003 1 96 17 17 ARG HB2 H 1.776 0.002 2 97 17 17 ARG HB3 H 1.648 0.003 2 98 17 17 ARG HG2 H 1.477 0.005 1 99 17 17 ARG HG3 H 1.477 0.005 1 100 17 17 ARG HD2 H 3.056 0.003 1 101 17 17 ARG HD3 H 3.056 0.003 1 102 17 17 ARG HE H 7.175 0.002 1 103 18 18 SER H H 8.422 0.002 1 104 18 18 SER HA H 4.482 0 1 105 18 18 SER HB2 H 3.906 0 1 106 18 18 SER HB3 H 3.906 0 1 107 19 19 SER H H 8.439 0.003 1 108 19 19 SER HA H 4.455 0.006 1 109 19 19 SER HB2 H 3.786 0 1 110 19 19 SER HB3 H 3.786 0 1 111 20 20 ILE H H 8.152 0.004 1 112 20 20 ILE HA H 4.140 0.003 1 113 20 20 ILE HB H 1.768 0.008 1 114 20 20 ILE HG12 H 1.393 0.007 1 115 20 20 ILE HG13 H 1.393 0.007 1 116 20 20 ILE HG2 H 0.806 0.004 1 117 20 20 ILE HD1 H 1.090 0.004 1 118 21 21 ALA H H 8.313 0.001 1 119 21 21 ALA HA H 4.280 0.004 1 120 21 21 ALA HB H 1.283 0.005 1 121 22 22 TYR H H 8.277 0.001 1 122 22 22 TYR HA H 4.485 0.003 1 123 22 22 TYR HB2 H 2.978 0.005 2 124 22 22 TYR HB3 H 2.948 0.005 2 125 22 22 TYR HD1 H 7.087 0.005 1 126 22 22 TYR HD2 H 7.087 0.005 1 127 22 22 TYR HE1 H 6.796 0.006 1 128 22 22 TYR HE2 H 6.796 0.006 1 129 23 23 GLY H H 8.372 0.002 1 130 23 23 GLY HA2 H 3.880 0 1 131 23 23 GLY HA3 H 3.880 0 1 132 24 24 GLY H H 7.801 0.007 1 133 24 24 GLY HA2 H 3.923 0.005 1 134 24 24 GLY HA3 H 3.923 0.005 1 135 25 25 GLY H H 8.160 0.002 1 136 25 25 GLY HA2 H 3.853 0 1 137 25 25 GLY HA3 H 3.853 0 1 stop_ save_