data_30428 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; CSP1-R3A ; _BMRB_accession_number 30428 _BMRB_flat_file_name bmr30428.str _Entry_type original _Submission_date 2018-03-12 _Accession_date 2018-03-12 _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 Yang Y. . . 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" 94 "13C chemical shifts" 31 "15N chemical shifts" 15 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-01-10 update BMRB 'update entry citation' 2018-08-22 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30427 CSP1-E1A 30429 CSP1-K6A 30430 CSP1-F11A stop_ _Original_release_date 2018-05-29 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Characterization of Competence-Stimulating Peptide Analogues Reveals Key Features for ComD1 and ComD2 Receptor Binding in Streptococcus pneumoniae ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30125091 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Yang Y. . . 2 Cornilescu G. . . 3 Tal-Gan Y. . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 57 _Journal_issue 36 _Journal_ISSN 1520-4995 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5359 _Page_last 5369 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Competence-stimulating peptide type 1' _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 'Competence-stimulating peptide type 1' _Molecular_mass 2162.619 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence ; EMALSKFFRDFILQRKK ; loop_ _Residue_seq_code _Residue_label 1 GLU 2 MET 3 ALA 4 LEU 5 SER 6 LYS 7 PHE 8 PHE 9 ARG 10 ASP 11 PHE 12 ILE 13 LEU 14 GLN 15 ARG 16 LYS 17 LYS 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 'Streptococcus pneumoniae' 1313 Bacteria . Streptococcus pneumoniae 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 '250 mM D DPC, 1.9 mM competence stimulating peptide type 1 mutant - CSP1R3A, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling DPC 250 mM 'natural abundance' $entity_1 1.9 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_5 _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' 0.15 . M pH 7.4 . pH pressure 1 . atm temperature 298 . 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 0.00 na indirect . . . 0.251449530 water H 1 protons ppm 4.771 na direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-15N HSQC' '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 2 2 MET HA H 4.449 0.00 . 2 2 2 MET HB2 H 2.064 0.00 . 3 2 2 MET HB3 H 2.033 0.00 . 4 2 2 MET HG2 H 2.575 0.00 . 5 2 2 MET CA C 53.257 0.00 . 6 3 3 ALA H H 8.773 0.00 . 7 3 3 ALA HA H 4.363 0.00 . 8 3 3 ALA HB H 1.413 0.00 . 9 3 3 ALA CA C 50.507 0.00 . 10 3 3 ALA CB C 16.124 0.00 . 11 3 3 ALA N N 127.415 0.00 . 12 4 4 LEU H H 8.755 0.00 . 13 4 4 LEU HA H 4.120 0.00 . 14 4 4 LEU HB2 H 1.767 0.00 . 15 4 4 LEU HB3 H 1.579 0.01 . 16 4 4 LEU HG H 1.720 0.00 . 17 4 4 LEU HD1 H 0.925 0.00 . 18 4 4 LEU HD2 H 0.838 0.00 . 19 4 4 LEU CA C 55.163 0.00 . 20 4 4 LEU CB C 39.581 0.00 . 21 4 4 LEU N N 120.818 0.00 . 22 5 5 SER H H 8.396 0.00 . 23 5 5 SER HA H 4.078 0.00 . 24 5 5 SER HB2 H 3.932 0.00 . 25 5 5 SER CA C 59.339 0.00 . 26 5 5 SER CB C 59.754 0.00 . 27 5 5 SER N N 113.861 0.00 . 28 6 6 LYS H H 7.557 0.00 . 29 6 6 LYS HA H 3.958 0.00 . 30 6 6 LYS HB2 H 1.852 0.00 . 31 6 6 LYS HB3 H 1.796 0.00 . 32 6 6 LYS HG2 H 1.369 0.00 . 33 6 6 LYS HG3 H 1.348 0.00 . 34 6 6 LYS HD2 H 1.409 0.00 . 35 6 6 LYS HE2 H 2.948 0.00 . 36 6 6 LYS CA C 56.745 0.00 . 37 6 6 LYS CB C 29.759 0.00 . 38 6 6 LYS N N 122.215 0.00 . 39 7 7 PHE H H 7.947 0.00 . 40 7 7 PHE HA H 4.313 0.00 . 41 7 7 PHE HB2 H 3.175 0.00 . 42 7 7 PHE HB3 H 3.060 0.00 . 43 7 7 PHE HE2 H 6.963 0.00 . 44 7 7 PHE CA C 58.405 0.00 . 45 7 7 PHE CB C 36.417 0.00 . 46 7 7 PHE N N 118.373 0.00 . 47 8 8 PHE H H 8.264 0.00 . 48 8 8 PHE HA H 4.124 0.00 . 49 8 8 PHE HB2 H 3.138 0.00 . 50 8 8 PHE HE2 H 7.204 0.00 . 51 8 8 PHE HZ H 7.162 0.00 . 52 8 8 PHE CA C 58.750 0.00 . 53 8 8 PHE CB C 36.871 0.00 . 54 8 8 PHE N N 117.377 0.00 . 55 9 9 ARG H H 8.273 0.00 . 56 9 9 ARG HA H 3.802 0.00 . 57 9 9 ARG HB2 H 1.929 0.00 . 58 9 9 ARG HB3 H 1.766 0.00 . 59 9 9 ARG HG2 H 1.559 0.00 . 60 9 9 ARG HD2 H 3.200 0.00 . 61 9 9 ARG HD3 H 3.168 0.00 . 62 9 9 ARG HE H 7.467 0.00 . 63 9 9 ARG CA C 57.485 0.00 . 64 9 9 ARG CB C 27.523 0.00 . 65 9 9 ARG N N 119.159 0.00 . 66 10 10 ASP H H 8.388 0.00 . 67 10 10 ASP HA H 4.280 0.00 . 68 10 10 ASP HB2 H 2.608 0.00 . 69 10 10 ASP HB3 H 2.320 0.00 . 70 10 10 ASP CA C 54.288 0.00 . 71 10 10 ASP CB C 37.488 0.00 . 72 10 10 ASP N N 117.659 0.00 . 73 11 11 PHE H H 7.937 0.00 . 74 11 11 PHE HA H 4.183 0.00 . 75 11 11 PHE HB2 H 2.885 0.00 . 76 11 11 PHE HB3 H 2.707 0.00 . 77 11 11 PHE HE2 H 7.050 0.01 . 78 11 11 PHE CA C 57.729 0.00 . 79 11 11 PHE CB C 37.053 0.00 . 80 11 11 PHE N N 118.331 0.00 . 81 12 12 ILE H H 7.675 0.00 . 82 12 12 ILE HA H 3.715 0.00 . 83 12 12 ILE HB H 1.907 0.00 . 84 12 12 ILE HG12 H 1.463 0.00 . 85 12 12 ILE HG13 H 1.170 0.00 . 86 12 12 ILE HG2 H 0.776 0.00 . 87 12 12 ILE HD1 H 0.740 0.00 . 88 12 12 ILE CA C 60.262 0.00 . 89 12 12 ILE CB C 34.808 0.00 . 90 12 12 ILE N N 116.784 0.00 . 91 13 13 LEU H H 7.932 0.00 . 92 13 13 LEU HA H 4.049 0.00 . 93 13 13 LEU HB2 H 1.776 0.00 . 94 13 13 LEU HB3 H 1.517 0.00 . 95 13 13 LEU HG H 1.607 0.00 . 96 13 13 LEU HD1 H 0.872 0.00 . 97 13 13 LEU HD2 H 0.817 0.00 . 98 13 13 LEU CA C 52.804 0.00 . 99 13 13 LEU CB C 39.097 0.00 . 100 13 13 LEU N N 118.227 0.00 . 101 14 14 GLN H H 7.658 0.00 . 102 14 14 GLN HA H 4.099 0.00 . 103 14 14 GLN HB2 H 2.017 0.00 . 104 14 14 GLN HB3 H 1.934 0.00 . 105 14 14 GLN HG2 H 2.280 0.00 . 106 14 14 GLN HG3 H 2.244 0.00 . 107 14 14 GLN HE22 H 7.408 0.00 . 108 14 14 GLN CA C 53.643 0.00 . 109 14 14 GLN CB C 25.819 0.00 . 110 14 14 GLN N N 116.484 0.00 . 111 15 15 ARG H H 7.638 0.00 . 112 15 15 ARG HA H 4.135 0.00 . 113 15 15 ARG HB2 H 1.755 0.00 . 114 15 15 ARG HB3 H 1.611 0.00 . 115 15 15 ARG HG2 H 1.487 0.00 . 116 15 15 ARG HG3 H 1.452 0.00 . 117 15 15 ARG HD2 H 2.984 0.00 . 118 15 15 ARG HD3 H 2.958 0.00 . 119 15 15 ARG HE H 7.399 0.00 . 120 15 15 ARG CA C 53.540 0.00 . 121 15 15 ARG CB C 27.818 0.00 . 122 15 15 ARG N N 119.434 0.00 . 123 16 16 LYS H H 8.035 0.00 . 124 16 16 LYS HA H 4.215 0.00 . 125 16 16 LYS HB2 H 1.801 0.00 . 126 16 16 LYS HB3 H 1.669 0.00 . 127 16 16 LYS HG2 H 1.388 0.00 . 128 16 16 LYS HD2 H 1.608 0.00 . 129 16 16 LYS CA C 53.650 0.00 . 130 16 16 LYS CB C 30.275 0.00 . 131 16 16 LYS N N 121.996 0.00 . 132 17 17 LYS H H 7.792 0.00 . 133 17 17 LYS HA H 4.044 0.00 . 134 17 17 LYS HB2 H 1.737 0.00 . 135 17 17 LYS HB3 H 1.641 0.00 . 136 17 17 LYS HG2 H 1.331 0.00 . 137 17 17 LYS HD2 H 1.599 0.00 . 138 17 17 LYS CA C 55.130 0.00 . 139 17 17 LYS CB C 30.949 0.00 . 140 17 17 LYS N N 127.796 0.00 . stop_ save_ save_spectral_peak_list_1 _Saveframe_category spectral_peak_list _Details . _Experiment_label '2D 1H-1H NOESY' _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 30428 >> _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 NOESY' >> _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 >>; >>Assignment w1 w2 >> >> Ala3N-HN 127.415 8.775 >> Leu4N-HN 120.818 8.756 >> Ser5N-HN 113.861 8.400 >> Lys6N-HN 122.215 7.557 >> Phe7N-HN 118.373 7.946 >> Phe8N-HN 117.377 8.268 >> Arg9N-HN 119.159 8.271 >> Asp10N-HN 117.659 8.389 >> Phe11N-HN 118.331 7.937 >> Ile12N-HN 116.784 7.679 >> Leu13N-HN 118.227 7.931 >> Gln14N-HN 116.484 7.659 >> Arg15N-HN 119.434 7.639 >> Lys16N-HN 121.996 8.035 >> Lys17N-HN 127.796 7.793 >>; >> >> 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 . . 9.0 ppm . . . 4.5 . . 30428 1 >> 2 . . H 1 H . . 10.0 ppm . . . 5.0 . . 30428 1 >> >> stop_ >> >>save_ >> ; save_