data_10117 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Confirmation of the Denatured Structure of Pyrrolidone carboxyl Peptidase under Non denaturing Conditions: Deference in Helix Propensity of Two Synthetic Peptides with Single Amino Acid Substitution ; _BMRB_accession_number 10117 _BMRB_flat_file_name bmr10117.str _Entry_type original _Submission_date 2007-02-16 _Accession_date 2007-02-17 _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 Umezaki Taro . . 2 Iimura Satoshi . . 3 Noda Yasuo . . 4 Segawa Shin-ichi . . 5 Yutani Katsuhide . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 89 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-27 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 10116 'PCP homo tetramer, mutant' stop_ _Original_release_date 2008-06-27 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The confirmation of the denatured structure of pyrrolidone carboxyl peptidase under nondenaturing conditions: difference in helix propensity of two synthetic peptides with single amino acid substitution. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17979195 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Umezaki Taro . . 2 Iimura Satoshi . . 3 Noda Yasuo . . 4 Segawa Shin-ichi . . 5 Yutani Katsuhide . . stop_ _Journal_abbreviation Proteins _Journal_volume 71 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 737 _Page_last 742 _Year 2008 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_citation_2 _Saveframe_category citation _Citation_full . _Citation_title ; Characterization of the denatured structure of pyrrolidone carboxyl peptidase from a hyperthermophile under nondenaturing conditions: role of the C-terminal alpha-helix of the protein in folding and stability. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17309236 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Iimura Satoshi . . 2 Umezaki Taro . . 3 Takeuchi Makoto . . 4 Mizuguchi Mineyuki . . 5 Yagi Hiromasa . . 6 Ogasahara Kyoko . . 7 Akutsu Hideo . . 8 Noda Yasuo . . 9 Segawa Shin-ichi . . 10 Yutani Katsuhide . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full . _Journal_volume 46 _Journal_issue 12 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 3664 _Page_last 3672 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'PCP homo tetramer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'subunit 1' $mutant_H6-peptide 'subunit 2' $mutant_H6-peptide 'subunit 3' $mutant_H6-peptide 'subunit 4' $mutant_H6-peptide stop_ _System_molecular_weight 91200 _System_physical_state native _System_oligomer_state 'protein-protein complex' _System_paramagnetic no _System_thiol_state 'free and disulfide bound' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'subunit 1' 1 'subunit 2' 1 'subunit 3' 1 'subunit 4' stop_ loop_ _Biological_function 'removal of N-terminal pyroglutamic acid from polypeptide' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_mutant_H6-peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'mutant H6-peptide' _Molecular_mass 2049 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence SYEMELEAVKVPIEVALE loop_ _Residue_seq_code _Residue_label 1 SER 2 TYR 3 GLU 4 MET 5 GLU 6 LEU 7 GLU 8 ALA 9 VAL 10 LYS 11 VAL 12 PRO 13 ILE 14 GLU 15 VAL 16 ALA 17 LEU 18 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-10-27 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 2EO8 "Crystal Structure Of A Mutant Pyrrolidone Carboxyl Peptidase (A199p) From P. Furiosus" 100.00 208 100.00 100.00 4.29e-01 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Fraction $mutant_H6-peptide 'Pyrococcus furiosus' 2261 Archaea . Pyrococcus furiosus yes 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 $mutant_H6-peptide '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 $mutant_H6-peptide 0.7 mM . '2.2.2 trifluoroethanol-d2' 30 % . stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name xwinnmr _Version . loop_ _Task collection stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Task 'peak assignments' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label $sample_1 save_ save_HOHAHA_2 _Saveframe_category NMR_applied_experiment _Experiment_name HOHAHA _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_1H-1H_NOESY _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_HOHAHA _Saveframe_category NMR_applied_experiment _Experiment_name HOHAHA _BMRB_pulse_sequence_accession_number . _Details . save_ save_DQF-COSY _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 0.02 pH temperature 298 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_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 0.015 external direct . . . 1.0 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_mutant_H6-peptide_30%TFE_pH7.0_25C _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '1H-1H NOESY' HOHAHA DQF-COSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $reference_1 _Mol_system_component_name 'subunit 1' _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 2 TYR HA H 4.57 0.01 1 2 2 2 TYR HB2 H 3.15 0.01 2 3 2 2 TYR HB3 H 3.07 0.01 2 4 2 2 TYR HD1 H 7.17 0.01 3 5 2 2 TYR HE1 H 6.88 0.01 3 6 3 3 GLU H H 8.86 0.01 1 7 3 3 GLU HA H 4.12 0.01 1 8 3 3 GLU HB2 H 2.04 0.01 2 9 3 3 GLU HB3 H 2.01 0.01 2 10 3 3 GLU HG2 H 2.37 0.01 2 11 3 3 GLU HG3 H 2.28 0.01 2 12 4 4 MET H H 8.04 0.01 1 13 4 4 MET HA H 4.38 0.01 1 14 4 4 MET HB2 H 2.16 0.01 2 15 4 4 MET HB3 H 2.10 0.01 2 16 4 4 MET HG2 H 2.65 0.01 2 17 4 4 MET HG3 H 2.59 0.01 2 18 5 5 GLU H H 8.35 0.01 1 19 5 5 GLU HA H 4.22 0.01 1 20 5 5 GLU HB2 H 2.11 0.01 2 21 5 5 GLU HG2 H 2.35 0.01 2 22 6 6 LEU H H 8.00 0.01 1 23 6 6 LEU HA H 4.27 0.01 1 24 6 6 LEU HB2 H 1.74 0.01 2 25 6 6 LEU HB3 H 1.62 0.01 2 26 6 6 LEU HG H 1.68 0.01 1 27 6 6 LEU HD1 H 0.93 0.01 2 28 6 6 LEU HD2 H 0.90 0.01 2 29 7 7 GLU H H 8.04 0.01 1 30 7 7 GLU HA H 4.19 0.01 1 31 7 7 GLU HB2 H 2.14 0.01 2 32 7 7 GLU HB3 H 2.07 0.01 2 33 8 8 ALA H H 7.94 0.01 1 34 8 8 ALA HA H 4.29 0.01 1 35 8 8 ALA HB H 1.49 0.01 1 36 9 9 VAL H H 7.68 0.01 1 37 9 9 VAL HA H 4.11 0.01 1 38 9 9 VAL HB H 2.21 0.01 1 39 9 9 VAL HG1 H 1.03 0.01 2 40 9 9 VAL HG2 H 0.98 0.01 2 41 10 10 LYS H H 7.98 0.01 1 42 10 10 LYS HA H 4.40 0.01 1 43 10 10 LYS HB2 H 1.87 0.01 2 44 10 10 LYS HB3 H 1.83 0.01 2 45 10 10 LYS HG2 H 1.51 0.01 2 46 10 10 LYS HG3 H 1.42 0.01 2 47 10 10 LYS HD2 H 1.72 0.01 2 48 10 10 LYS HE2 H 3.02 0.01 2 49 11 11 VAL H H 7.88 0.01 1 50 11 11 VAL HA H 4.42 0.01 1 51 11 11 VAL HB H 2.13 0.01 1 52 11 11 VAL HG1 H 1.01 0.01 2 53 11 11 VAL HG2 H 1.00 0.01 2 54 12 12 PRO HA H 4.52 0.01 1 55 12 12 PRO HB2 H 2.32 0.01 2 56 12 12 PRO HB3 H 2.04 0.01 2 57 12 12 PRO HG2 H 2.10 0.01 2 58 12 12 PRO HD2 H 3.90 0.01 2 59 12 12 PRO HD3 H 3.67 0.01 2 60 13 13 ILE H H 7.91 0.01 1 61 13 13 ILE HA H 4.15 0.01 1 62 13 13 ILE HB H 1.90 0.01 1 63 13 13 ILE HG12 H 1.54 0.01 2 64 13 13 ILE HG13 H 1.24 0.01 2 65 13 13 ILE HG2 H 1.45 0.01 1 66 13 13 ILE HD1 H 0.93 0.01 1 67 14 14 GLU H H 8.64 0.01 1 68 14 14 GLU HA H 4.27 0.01 1 69 14 14 GLU HB2 H 2.07 0.01 2 70 14 14 GLU HB3 H 2.01 0.01 2 71 14 14 GLU HG2 H 2.21 0.01 2 72 15 15 VAL H H 7.83 0.01 1 73 15 15 VAL HA H 4.13 0.01 1 74 15 15 VAL HB H 2.14 0.01 1 75 15 15 VAL HG1 H 0.98 0.01 2 76 15 15 VAL HG2 H 0.96 0.01 2 77 16 16 ALA H H 8.07 0.01 1 78 16 16 ALA HA H 4.40 0.01 1 79 16 16 ALA HB H 1.44 0.01 1 80 17 17 LEU H H 8.02 0.01 1 81 17 17 LEU HA H 4.41 0.01 1 82 17 17 LEU HB2 H 1.73 0.01 2 83 17 17 LEU HG H 1.73 0.01 1 84 17 17 LEU HD1 H 0.96 0.01 2 85 17 17 LEU HD2 H 0.90 0.01 2 86 18 18 GLU H H 7.67 0.01 1 87 18 18 GLU HA H 4.17 0.01 1 88 18 18 GLU HB2 H 2.26 0.01 2 89 18 18 GLU HB3 H 1.97 0.01 2 stop_ save_