data_15392 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Tetrameric structure of KIA7F peptide ; _BMRB_accession_number 15392 _BMRB_flat_file_name bmr15392.str _Entry_type new _Submission_date 2007-07-19 _Accession_date 2007-07-19 _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 'lopez de la Osa' Jaime . . 2 Gonzalez Carlos . . 3 Laurents Douglas V. . 4 Chakrabartty Avijit . . 5 Bateman David A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 103 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-03-13 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 15391 'KIA7 temramer' stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_title ; Getting specificity from simplicity in putative proteins from the prebiotic earth. ; _Citation_status published _Citation_type journal _PubMed_ID 17855563 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 'Lopez de la Osa' Jaime . Sr. 2 Gonzalez Carlos . Sr. 3 Laurents Douglas V. Sr. 4 Chakrabartty Avijit . Sr. 5 Ho S. . Sr. 5 Bateman David A. Sr. stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_volume 104 _Journal_issue 38 _Page_first 14941 _Page_last 14946 _Year 2007 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'KIA7F peptide tetramer' loop_ _Mol_system_component_name _Mol_label 'KIA7F peptide, chain 1' $KIA7F 'KIA7F peptide, chain 2' $KIA7F 'KIA7F peptide, chain 3' $KIA7F 'KIA7F peptide, chain 4' $KIA7F stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_KIA7F _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common KIA7F _Molecular_mass 1853.298 _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence XKAAAAAIKAIAAIIKAGGX loop_ _Residue_seq_code _Residue_label 1 ALA_AC 2 LYS 3 ALA 4 ALA 5 ALA 6 ALA 7 ALA 8 ILE 9 LYS 10 ALA 11 ILE 12 ALA 13 ALA 14 ILE 15 ILE 16 LYS 17 ALA 18 GLY 19 GLY 20 NFA stop_ save_ ###################### # Polymer residues # ###################### save_ALA_AC _Saveframe_category polymer_residue _Mol_type complete _Name_common 'N-ACETYL ALANINE' _BMRB_code ALA_AC _Standard_residue_derivative ALA loop_ _Mol_label _Residue_seq_code $KIA7F 1 stop_ _Mol_empirical_formula 'C5 H8 N1 O2' _Mol_paramagnetic no loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N . N . 0 . ? CA . C . 0 . ? CB . C . 0 . ? C . C . 0 . ? C1 . C . 0 . ? C2 . C . 0 . ? O1 . O . 0 . ? O . O . 0 . ? H . H . 0 . ? HA . H . 0 . ? HB1 . H . 0 . ? HB2 . H . 0 . ? HB3 . H . 0 . ? H21 . H . 0 . ? H22 . H . 0 . ? H23 . H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA . . SING N C1 . . SING N H . . SING CA CB . . SING CA C . . SING CA HA . . SING CB HB1 . . SING CB HB2 . . SING CB HB3 . . DOUB C O . . DOUB C1 O1 . . SING C1 C2 . . SING C2 H21 . . SING C2 H22 . . SING C2 H23 . . stop_ save_ save_chem_comp_NFA _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 'PHENYLALANINE AMIDE' _PDB_code NFA _Standard_residue_derivative . _Mol_empirical_formula 'C9 H12 N2 O' _Molecular_mass 164.204 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 21 23:31:31 2007 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N N 0 . ? CA CA C S 0 . ? C C C N 0 . ? O O O N 0 . ? CB CB C N 0 . ? CG CG C N 0 . ? CD1 CD1 C N 0 . ? CD2 CD2 C N 0 . ? CE1 CE1 C N 0 . ? CE2 CE2 C N 0 . ? CZ CZ C N 0 . ? NXT NXT N N 0 . ? H H H N 0 . ? HN2 HN2 H N 0 . ? HA HA H N 0 . ? HB1 HB1 H N 0 . ? HB2 HB2 H N 0 . ? HD1 HD1 H N 0 . ? HD2 HD2 H N 0 . ? HE1 HE1 H N 0 . ? HE2 HE2 H N 0 . ? HZ HZ H N 0 . ? HXT1 HXT1 H N 0 . ? HXT2 HXT2 H N 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA N CA SING N H N H SING N HN2 N HN2 SING CA C CA C SING CA CB CA CB SING CA HA CA HA DOUB C O C O SING C NXT C NXT SING CB CG CB CG SING CB HB1 CB HB1 SING CB HB2 CB HB2 DOUB CG CD1 CG CD1 SING CG CD2 CG CD2 SING CD1 CE1 CD1 CE1 SING CD1 HD1 CD1 HD1 DOUB CD2 CE2 CD2 CE2 SING CD2 HD2 CD2 HD2 DOUB CE1 CZ CE1 CZ SING CE1 HE1 CE1 HE1 SING CE2 CZ CE2 CZ SING CE2 HE2 CE2 HE2 SING CZ HZ CZ HZ SING NXT HXT1 NXT HXT1 SING NXT HXT2 NXT HXT2 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $KIA7F . . . . . . 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 $KIA7F 'chemical synthesis' . . . . ? stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_KIA7F_sample _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $KIA7F 10 mM 'natural abundance' 'sodium chloride' 200 mM 'natural abundance' DSS 0.005 mM 'natural abundance' H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ save_ save_AMBER _Saveframe_category software _Name AMBER _Version 7.0 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Koll' . . stop_ loop_ _Task refinement stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details Cryoprobe save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $KIA7F save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $KIA7F save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $KIA7F save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278.15 . K pH 5.0 . pH pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_KIA7FBRMBlist _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 ? ? ? 1.000000000 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 loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D DQF-COSY' stop_ loop_ _Sample_label $KIA7F stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $KIA7FBRMBlist _Mol_system_component_name 'KIA7F peptide, chain 1' 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 ALA_AC HA H 4.17 0.01 1 2 2 2 LYS H H 8.60 0.01 1 3 2 2 LYS HA H 4.23 0.01 1 4 2 2 LYS HB2 H 1.93 0.01 1 5 2 2 LYS HB3 H 1.61 0.01 1 6 2 2 LYS HD2 H 1.74 0.01 2 7 2 2 LYS HD3 H 1.74 0.01 2 8 2 2 LYS HE2 H 3.03 0.01 2 9 2 2 LYS HE3 H 3.03 0.01 2 10 2 2 LYS HG2 H 1.51 0.01 2 11 2 2 LYS HG3 H 1.51 0.01 2 12 3 3 ALA H H 8.38 0.01 1 13 3 3 ALA HA H 4.38 0.01 1 14 3 3 ALA HB H 1.65 0.01 1 15 4 4 ALA H H 8.63 0.01 1 16 4 4 ALA HA H 3.85 0.01 1 17 4 4 ALA HB H 1.36 0.01 1 18 5 5 ALA H H 8.35 0.01 1 19 5 5 ALA HA H 3.85 0.01 1 20 5 5 ALA HB H 1.52 0.01 1 21 6 6 ALA H H 7.91 0.01 1 22 6 6 ALA HA H 4.19 0.01 1 23 6 6 ALA HB H 1.55 0.01 1 24 7 7 ALA H H 8.05 0.01 1 25 7 7 ALA HA H 4.26 0.01 1 26 7 7 ALA HB H 1.32 0.01 1 27 8 8 ILE H H 8.37 0.01 1 28 8 8 ILE HA H 3.63 0.01 1 29 8 8 ILE HB H 1.60 0.01 1 30 8 8 ILE HD1 H 0.52 0.01 1 31 8 8 ILE HG12 H 0.94 0.01 2 32 8 8 ILE HG13 H 0.94 0.01 2 33 8 8 ILE HG2 H 0.27 0.01 1 34 9 9 LYS H H 7.63 0.01 1 35 9 9 LYS HA H 4.02 0.01 1 36 9 9 LYS HB2 H 1.97 0.01 1 37 9 9 LYS HB3 H 1.66 0.01 1 38 9 9 LYS HD2 H 1.75 0.01 2 39 9 9 LYS HD3 H 1.75 0.01 2 40 9 9 LYS HE2 H 3.04 0.01 2 41 9 9 LYS HE3 H 3.04 0.01 2 42 9 9 LYS HG2 H 1.48 0.01 2 43 9 9 LYS HG3 H 1.48 0.01 2 44 9 9 LYS HZ H 7.67 0.01 1 45 10 10 ALA H H 7.81 0.01 1 46 10 10 ALA HA H 4.26 0.01 1 47 10 10 ALA HB H 1.61 0.01 1 48 11 11 ILE H H 8.53 0.01 1 49 11 11 ILE HA H 3.57 0.01 1 50 11 11 ILE HB H 2.21 0.01 1 51 11 11 ILE HD1 H 0.91 0.01 1 52 11 11 ILE HG12 H 1.85 0.01 1 53 11 11 ILE HG13 H 1.61 0.01 1 54 11 11 ILE HG2 H 0.79 0.01 1 55 12 12 ALA H H 9.09 0.01 1 56 12 12 ALA HA H 3.89 0.01 1 57 12 12 ALA HB H 1.53 0.01 1 58 13 13 ALA H H 7.88 0.01 1 59 13 13 ALA HA H 4.26 0.01 1 60 13 13 ALA HB H 1.59 0.01 1 61 14 14 ILE H H 7.47 0.01 1 62 14 14 ILE HA H 3.81 0.01 1 63 14 14 ILE HB H 2.11 0.01 1 64 14 14 ILE HD1 H 0.83 0.01 1 65 14 14 ILE HG12 H 1.81 0.01 1 66 14 14 ILE HG13 H 1.21 0.01 1 67 14 14 ILE HG2 H 1.03 0.01 1 68 15 15 ILE H H 8.06 0.01 1 69 15 15 ILE HA H 4.02 0.01 1 70 15 15 ILE HB H 2.35 0.01 1 71 15 15 ILE HD1 H 0.69 0.01 1 72 15 15 ILE HG12 H 1.71 0.01 1 73 15 15 ILE HG13 H 1.33 0.01 1 74 15 15 ILE HG2 H 1.02 0.01 1 75 16 16 LYS H H 8.59 0.01 1 76 16 16 LYS HA H 4.16 0.01 1 77 16 16 LYS HB2 H 1.92 0.01 1 78 16 16 LYS HB3 H 2.00 0.01 1 79 16 16 LYS HD2 H 1.72 0.01 2 80 16 16 LYS HD3 H 1.72 0.01 2 81 16 16 LYS HE2 H 2.99 0.01 2 82 16 16 LYS HE3 H 2.99 0.01 2 83 16 16 LYS HG2 H 1.53 0.01 1 84 16 16 LYS HG3 H 1.43 0.01 1 85 16 16 LYS HZ H 7.63 0.01 1 86 17 17 ALA H H 8.45 0.01 1 87 17 17 ALA HA H 4.16 0.01 1 88 17 17 ALA HB H 1.53 0.01 1 89 18 18 GLY H H 7.57 0.01 1 90 18 18 GLY HA2 H 4.03 0.01 1 91 18 18 GLY HA3 H 3.36 0.01 1 92 19 19 GLY H H 7.61 0.01 1 93 19 19 GLY HA2 H 3.87 0.01 1 94 19 19 GLY HA3 H 3.77 0.01 1 95 20 20 NFA H H 7.55 0.01 1 96 20 20 NFA HA H 4.49 0.01 1 97 20 20 NFA HB2 H 3.24 0.01 1 98 20 20 NFA HB3 H 2.77 0.01 1 99 20 20 NFA HD1 H 7.06 0.01 3 100 20 20 NFA HD2 H 7.06 0.01 3 101 20 20 NFA HE1 H 7.39 0.01 3 102 20 20 NFA HE2 H 7.39 0.01 3 103 20 20 NFA HZ H 7.30 0.01 1 stop_ save_