data_30476 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the cyclic tetrapeptide, PYPV ; _BMRB_accession_number 30476 _BMRB_flat_file_name bmr30476.str _Entry_type original _Submission_date 2018-06-08 _Accession_date 2018-06-08 _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 Shekhtman A. . . 2 Breindel L. . . 3 Zhang Q. . . 4 Chen H. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 spectral_peak_list 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 26 "13C chemical shifts" 16 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-06-07 original BMRB . stop_ _Original_release_date 2018-06-18 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution structure of the cyclic tetrapeptide, PYPV. ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Shekhtman A. . . 2 Breindel L. . . 3 Zhang Q. . . 4 Chen H. . . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Cyclic tetrapeptide PYPV' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Cyclic tetrapeptide PYPV' _Molecular_mass 474.549 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence ; PYPV ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 TYR 3 PRO 4 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 'Lactobacillus helveticus' 1587 Bacteria . Lactobacillus helveticus 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_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 mM NA cyclo(-L-Pro-L-Tyr-L-Pro-L-Val-), deuterated DMSO' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version 3.96 loop_ _Vendor _Address _Electronic_address 'Guntert P.' . . 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CARA _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . 'Keller, Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III' _Field_strength 600 _Details . 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-1H_ROESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _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 _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 0.2 'Not defined' pH 7.0 0.1 pH* pressure 1 0.01 bar temperature 293 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal 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_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-1H ROESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 1 1 PRO HA H 4.047 0.020 1 2 1 1 PRO HB2 H 1.803 0.020 2 3 1 1 PRO HB3 H 1.632 0.020 2 4 1 1 PRO HG2 H 1.637 0.020 2 5 1 1 PRO HG3 H 1.248 0.020 2 6 1 1 PRO HD2 H 3.429 0.020 2 7 1 1 PRO HD3 H 3.103 0.020 2 8 1 1 PRO CA C 61.379 0.3 1 9 1 1 PRO CB C 31.287 0.3 1 10 1 1 PRO CG C 21.210 0.3 1 11 1 1 PRO CD C 46.669 0.3 1 12 2 2 TYR H H 7.988 0.020 1 13 2 2 TYR HA H 4.863 0.020 1 14 2 2 TYR HB2 H 3.009 0.020 2 15 2 2 TYR HB3 H 2.537 0.020 2 16 2 2 TYR HD1 H 6.950 0.020 1 17 2 2 TYR HD2 H 6.950 0.020 1 18 2 2 TYR HE1 H 6.584 0.020 1 19 2 2 TYR HE2 H 6.584 0.020 1 20 2 2 TYR CA C 51.743 0.3 1 21 2 2 TYR CB C 37.108 0.3 1 22 2 2 TYR CD1 C 130.500 0.3 1 23 2 2 TYR CD2 C 130.500 0.3 1 24 2 2 TYR CE1 C 114.600 0.3 1 25 2 2 TYR CE2 C 114.600 0.3 1 26 3 3 PRO HA H 4.243 0.020 1 27 3 3 PRO HB2 H 2.045 0.020 2 28 3 3 PRO HB3 H 1.960 0.020 2 29 3 3 PRO HG2 H 1.889 0.020 2 30 3 3 PRO HG3 H 1.523 0.020 2 31 3 3 PRO HD2 H 3.558 0.020 2 32 3 3 PRO HD3 H 3.205 0.020 2 33 3 3 PRO CA C 61.565 0.3 1 34 3 3 PRO CB C 31.808 0.3 1 35 3 3 PRO CG C 21.934 0.3 1 36 3 3 PRO CD C 47.025 0.3 1 37 4 4 VAL H H 7.841 0.020 1 38 4 4 VAL HA H 4.407 0.020 1 39 4 4 VAL HG1 H 0.787 0.020 2 40 4 4 VAL HG2 H 0.817 0.020 2 41 4 4 VAL CA C 55.120 0.3 1 42 4 4 VAL CB C 29.073 0.3 1 stop_ save_ save_spectral_peak_list_1 _Saveframe_category spectral_peak_list _Details . _Experiment_label '2D 1H-1H ROESY' _Number_of_spectral_dimensions 2 loop_ _Expt_dimension_ID _Atom_type _Spectral_region 1 H H 2 H H stop_ _Sample_label $sample_1 _Sample_conditions_label $sample_conditions_1 _Text_data_format "NMR-STAR v3" _Text_data ; >>save_spectral_peak_list_1 >> _Spectral_peak_list.Sf_category spectral_peak_list >> _Spectral_peak_list.Sf_framecode spectral_peak_list_1 >> _Spectral_peak_list.Entry_ID 30476 >> _Spectral_peak_list.ID 1 >> _Spectral_peak_list.Sample_ID 1 >> _Spectral_peak_list.Sample_label $sample_1 >> _Spectral_peak_list.Sample_condition_list_ID 1 >> _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 >> _Spectral_peak_list.Experiment_ID 3 >> _Spectral_peak_list.Experiment_name '2D 1H-1H ROESY' >> _Spectral_peak_list.Experiment_class . >> _Spectral_peak_list.Experiment_type . >> _Spectral_peak_list.Number_of_spectral_dimensions 2 >> _Spectral_peak_list.Chemical_shift_list . >> _Spectral_peak_list.Assigned_chem_shift_list_ID 1 >> _Spectral_peak_list.Assigned_chem_shift_list_label $assigned_chemical_shifts_1 >> _Spectral_peak_list.Details . >> _Spectral_peak_list.Text_data_format text >> _Spectral_peak_list.Text_data >>; >># Number of dimensions 2 >># FORMAT xeasy2D >># INAME 1 H1 >># INAME 2 H2 >># SPECTRUM NOESY H1 H2 >> 2 1.960 7.841 0 U 9.632e+001 0.00e+000 - 0 46 11 0 >># HB3 P3/H V4 >> 4 1.960 4.863 0 U 1.360e+001 0.00e+000 - 0 46 1 0 >># HB3 P3/HA Y2 >> 13 0.817 4.047 0 U 4.552e+002 0.00e+000 - 0 24 5 0 >># HG2 V4/HA P1 >> 14 0.820 3.111 0 U 1.117e+002 0.00e+000 - 0 24 39 0 >># HG2 V4/HD3 P1 >> 16 7.843 1.956 0 U 3.036e+002 0.00e+000 - 0 11 46 0 >># H V4/HB3 P3 >> 20 7.841 4.046 0 U 5.171e+002 0.00e+000 - 0 11 5 0 >># H V4/HA P1 >> 21 7.841 3.103 0 U 2.280e+000 0.00e+000 - 0 11 39 0 >># H V4/HD3 P1 >> 22 7.841 7.988 0 U 8.861e+003 0.00e+000 - 0 11 10 0 >># H V4/H Y2 >> 23 7.842 4.241 0 U 1.086e+003 0.00e+000 - 0 11 7 0 >># H V4/HA P3 >> 29 6.950 3.558 0 U 8.228e+002 0.00e+000 - 0 27 36 0 >># HD Y2/HD2 P3 >> 34 3.205 4.863 0 U 4.340e+001 0.00e+000 - 0 37 1 0 >># HD3 P3/HA Y2 >> 43 4.409 4.047 0 U 1.889e+004 0.00e+000 - 0 3 5 0 >># HA V4/HA P1 >> 44 4.406 7.986 0 U 3.418e+002 0.00e+000 - 0 3 10 0 >># HA V4/H Y2 >> 53 4.863 1.948 0 U 2.204e+002 0.00e+000 - 0 1 46 0 >># HA Y2/HB3 P3 >> 55 4.863 3.205 0 U 2.572e+001 0.00e+000 - 0 1 37 0 >># HA Y2/HD3 P3 >> 59 4.863 4.239 0 U 1.419e+004 0.00e+000 - 0 1 7 0 >># HA Y2/HA P3 >> 62 4.047 0.809 0 U 2.592e+002 0.00e+000 - 0 5 24 0 >># HA P1/HG2 V4 >> 63 4.047 7.835 0 U 8.824e+002 0.00e+000 - 0 5 11 0 >># HA P1/H V4 >> 64 4.051 4.407 0 U 1.776e+004 0.00e+000 - 0 5 3 0 >># HA P1/HA V4 >> 69 4.049 7.989 0 U 1.041e+003 0.00e+000 - 0 5 10 0 >># HA P1/H Y2 >> 71 4.047 0.796 0 U 2.324e+002 0.00e+000 - 0 5 75 0 >># HA P1/HG1 V4 >> 81 3.103 0.817 0 U 1.822e+002 0.00e+000 - 0 39 24 0 >># HD3 P1/HG2 V4 >> 82 3.103 7.841 0 U 3.066e+002 0.00e+000 - 0 39 11 0 >># HD3 P1/H V4 >> 87 3.103 7.988 0 U 1.433e+003 0.00e+000 - 0 39 10 0 >># HD3 P1/H Y2 >> 97 7.988 7.841 0 U 7.817e+003 0.00e+000 - 0 10 11 0 >># H Y2/H V4 >> 99 7.988 4.407 0 U 5.572e+001 0.00e+000 - 0 10 3 0 >># H Y2/HA V4 >> 101 7.987 4.044 0 U 1.285e+003 0.00e+000 - 0 10 5 0 >># H Y2/HA P1 >> 102 7.988 3.103 0 U 1.994e+003 0.00e+000 - 0 10 39 0 >># H Y2/HD3 P1 >>105 7.987 1.652 0 U 3.902e+002 0.00e+000 - 0 10 47 0 >># H Y2/HB3 P1 >> 106 7.988 1.522 0 U 1.004e+001 0.00e+000 - 0 10 40 0 >># H Y2/HG3 P3 >> 107 7.987 4.243 0 U 6.649e+002 0.00e+000 - 0 10 7 0 >># H Y2/HA P3 >> 111 3.544 6.963 0 U 1.788e+001 0.00e+000 - 0 36 27 0 >># HD2 P3/HD Y2 >> 151 4.240 4.863 0 U 1.493e+004 0.00e+000 - 0 7 1 0 >># HA P3/HA Y2 >> 161 0.787 4.047 0 U 1.670e+003 0.00e+000 - 0 75 5 0 >># HG1 V4/HA P1 >>; >> >> loop_ >> _Spectral_dim.ID >> _Spectral_dim.Axis_code >> _Spectral_dim.Spectrometer_frequency >> _Spectral_dim.Atom_type >> _Spectral_dim.Atom_isotope_number >> _Spectral_dim.Spectral_region >> _Spectral_dim.Magnetization_linkage_ID >> _Spectral_dim.Under_sampling_type >> _Spectral_dim.Sweep_width >> _Spectral_dim.Sweep_width_units >> _Spectral_dim.Value_first_point >> _Spectral_dim.Absolute_peak_positions >> _Spectral_dim.Acquisition >> _Spectral_dim.Center_frequency_offset >> _Spectral_dim.Encoding_code >> _Spectral_dim.Encoded_reduced_dimension_ID >> _Spectral_dim.Entry_ID >> _Spectral_dim.Spectral_peak_list_ID >> >> 1 . . H 1 H 2 . 12 ppm . . . 4.701 . . 30476 1 >> 2 . . H 1 H 1 . 12 ppm . . . 4.701 . . 30476 1 >> >> stop_ >> >>save_ >> ; save_