data_11003 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of the antimicrobial peptide RP-1 bound to DPC micelles ; _BMRB_accession_number 11003 _BMRB_flat_file_name bmr11003.str _Entry_type new _Submission_date 2007-07-07 _Accession_date 2007-07-07 _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 Bourbigot Sarah . . 2 Booth Valerie . . 3 Dodd Erin . . 4 Horwood Chrystal . . 5 Welch William H. . 6 Sharma Shantanu . . 7 Waring Alan J. . 8 Yeaman Michael R. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 139 "15N chemical shifts" 5 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-08-25 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title 'Antimicrobial peptide RP-1 structure and interactions with anionic versus zwitterionic micelles.' _Citation_status published _Citation_type journal _PubMed_ID 18712851 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bourbigot Sarah . . 2 Dodd Erin . . 3 Horwood Chrystal . . 4 Cumby Nichole . . 5 Fardy Liam . . 6 Welch William H. . 7 Ramjan Zachary . . 8 Sharma Shantanu . . 9 Waring Alan J. . 10 Yeaman Michael R. . 11 Booth Valerie . . stop_ _Journal_abbreviation Biopolymers. _Journal_volume . _Journal_issue . _Page_first . _Page_last . _Year 2008 loop_ _Keyword nmr 'antimicrobial peptide' micelles RP-1 stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'antimicrobial peptide RP-1' loop_ _Mol_system_component_name _Mol_label 'subunit 1' $entity stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2170.836 _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ALYKKFKKKLLKSLKRLG loop_ _Residue_seq_code _Residue_label 1 ALA 2 LEU 3 TYR 4 LYS 5 LYS 6 PHE 7 LYS 8 LYS 9 LYS 10 LEU 11 LEU 12 LYS 13 SER 14 LEU 15 LYS 16 ARG 17 LEU 18 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-31 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 BMRB 11002 "antimicrobial peptide RP-1 subunit 1" 100.00 18 100.00 100.00 2.74e+00 PDB 2RLG "Nmr Structure Of The Antimicrobial Peptide Rp-1 Bound To Sds Micelles" 100.00 18 100.00 100.00 2.74e+00 PDB 2RLH "Nmr Structure Of The Antimicrobial Peptide Rp-1 Bound To Dpc Micelles" 100.00 18 100.00 100.00 2.74e+00 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 _Details $entity 'chemical synthesis' . . . . ? 'solid phase synthesis employing Fmoc (O-fluorenylmethyl-oxycarbonyl) chemistry' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 1.5 mM [U-15N]-Leu DSS 0.4 mM 'natural abundance' DPC 150 mM '[U-99% 2H]' 'sodium azide' 0.4 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' 'peak picking' stop_ save_ save_NMRPipe _Saveframe_category software _Name NMRPipe loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 313 . K pH 5 . pH pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _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 DSS N 15 'methyl protons' ppm 0.00 n/a 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-1H NOESY' 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 'subunit 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 HB H 1.550 0.020 1 2 2 2 LEU H H 8.640 0.020 1 3 2 2 LEU HA H 4.150 0.020 1 4 2 2 LEU HB2 H 1.630 0.020 2 5 2 2 LEU HB3 H 1.710 0.020 2 6 2 2 LEU HG H 1.760 0.020 1 7 2 2 LEU HD1 H 0.870 0.020 2 8 2 2 LEU HD2 H 0.930 0.020 2 9 2 2 LEU N N 120.670 0.500 1 10 3 3 TYR H H 8.810 0.020 1 11 3 3 TYR HA H 4.220 0.020 1 12 3 3 TYR HB2 H 3.110 0.020 1 13 3 3 TYR HB3 H 3.110 0.020 1 14 3 3 TYR HD1 H 7.020 0.020 1 15 3 3 TYR HD2 H 7.020 0.020 1 16 3 3 TYR HE1 H 6.790 0.020 1 17 3 3 TYR HE2 H 6.790 0.020 1 18 4 4 LYS H H 7.810 0.020 1 19 4 4 LYS HA H 3.770 0.020 1 20 4 4 LYS HB2 H 1.690 0.020 2 21 4 4 LYS HB3 H 1.820 0.020 2 22 4 4 LYS HG2 H 1.360 0.020 1 23 4 4 LYS HG3 H 1.360 0.020 1 24 4 4 LYS HD2 H 1.470 0.020 1 25 4 4 LYS HD3 H 1.470 0.020 1 26 4 4 LYS HE2 H 3.100 0.020 1 27 4 4 LYS HE3 H 3.100 0.020 1 28 5 5 LYS H H 7.700 0.020 1 29 5 5 LYS HA H 4.010 0.020 1 30 5 5 LYS HB2 H 1.800 0.020 2 31 5 5 LYS HB3 H 1.880 0.020 2 32 5 5 LYS HG2 H 1.480 0.020 1 33 5 5 LYS HG3 H 1.480 0.020 1 34 5 5 LYS HD2 H 1.610 0.020 1 35 5 5 LYS HD3 H 1.610 0.020 1 36 5 5 LYS HE2 H 2.890 0.020 1 37 5 5 LYS HE3 H 2.890 0.020 1 38 6 6 PHE H H 8.210 0.020 1 39 6 6 PHE HA H 4.280 0.020 1 40 6 6 PHE HB2 H 3.140 0.020 2 41 6 6 PHE HB3 H 3.200 0.020 2 42 6 6 PHE HD1 H 7.150 0.020 1 43 6 6 PHE HD2 H 7.150 0.020 1 44 6 6 PHE HE1 H 7.210 0.020 1 45 6 6 PHE HE2 H 7.210 0.020 1 46 6 6 PHE HZ H 7.030 0.020 1 47 7 7 LYS H H 8.340 0.020 1 48 7 7 LYS HA H 3.630 0.020 1 49 7 7 LYS HB2 H 1.630 0.020 2 50 7 7 LYS HB3 H 1.720 0.020 2 51 7 7 LYS HG2 H 1.260 0.020 1 52 7 7 LYS HG3 H 1.260 0.020 1 53 7 7 LYS HD2 H 1.310 0.020 1 54 7 7 LYS HD3 H 1.310 0.020 1 55 7 7 LYS HE2 H 2.810 0.020 1 56 7 7 LYS HE3 H 2.810 0.020 1 57 8 8 LYS H H 7.780 0.020 1 58 8 8 LYS HA H 3.940 0.020 1 59 8 8 LYS HB2 H 1.690 0.020 2 60 8 8 LYS HB3 H 1.920 0.020 2 61 8 8 LYS HG2 H 1.440 0.020 1 62 8 8 LYS HG3 H 1.440 0.020 1 63 8 8 LYS HD2 H 1.490 0.020 1 64 8 8 LYS HD3 H 1.490 0.020 1 65 8 8 LYS HE2 H 2.960 0.020 1 66 8 8 LYS HE3 H 2.960 0.020 1 67 9 9 LYS H H 7.640 0.020 1 68 9 9 LYS HA H 4.050 0.020 1 69 9 9 LYS HB2 H 1.870 0.020 2 70 9 9 LYS HB3 H 1.920 0.020 2 71 9 9 LYS HG2 H 1.470 0.020 1 72 9 9 LYS HG3 H 1.470 0.020 1 73 9 9 LYS HD2 H 1.660 0.020 1 74 9 9 LYS HD3 H 1.660 0.020 1 75 9 9 LYS HE2 H 2.870 0.020 1 76 9 9 LYS HE3 H 2.870 0.020 1 77 10 10 LEU H H 8.240 0.020 1 78 10 10 LEU HA H 3.950 0.020 1 79 10 10 LEU HB2 H 1.610 0.020 2 80 10 10 LEU HB3 H 1.660 0.020 2 81 10 10 LEU HG H 1.480 0.020 1 82 10 10 LEU HD1 H 0.820 0.020 1 83 10 10 LEU HD2 H 0.820 0.020 1 84 10 10 LEU N N 120.600 0.500 1 85 11 11 LEU H H 8.150 0.020 1 86 11 11 LEU HA H 3.950 0.020 1 87 11 11 LEU HB2 H 1.810 0.020 1 88 11 11 LEU HB3 H 1.810 0.020 1 89 11 11 LEU HG H 1.550 0.020 1 90 11 11 LEU HD1 H 0.920 0.020 1 91 11 11 LEU HD2 H 0.920 0.020 1 92 11 11 LEU N N 117.730 0.500 1 93 12 12 LYS H H 7.760 0.020 1 94 12 12 LYS HA H 4.060 0.020 1 95 12 12 LYS HB2 H 1.910 0.020 2 96 12 12 LYS HB3 H 1.950 0.020 2 97 12 12 LYS HG2 H 1.550 0.020 1 98 12 12 LYS HG3 H 1.550 0.020 1 99 12 12 LYS HD2 H 1.710 0.020 1 100 12 12 LYS HD3 H 1.710 0.020 1 101 12 12 LYS HE2 H 2.970 0.020 1 102 12 12 LYS HE3 H 2.970 0.020 1 103 13 13 SER H H 7.800 0.020 1 104 13 13 SER HA H 4.280 0.020 1 105 13 13 SER HB2 H 3.860 0.020 2 106 13 13 SER HB3 H 3.970 0.020 2 107 14 14 LEU H H 7.820 0.020 1 108 14 14 LEU HA H 4.150 0.020 1 109 14 14 LEU HB2 H 1.830 0.020 1 110 14 14 LEU HB3 H 1.830 0.020 1 111 14 14 LEU HG H 1.600 0.020 1 112 14 14 LEU HD1 H 0.870 0.020 1 113 14 14 LEU HD2 H 0.870 0.020 1 114 14 14 LEU N N 119.780 0.500 1 115 15 15 LYS H H 7.680 0.020 1 116 15 15 LYS HA H 4.150 0.020 1 117 15 15 LYS HB2 H 1.910 0.020 2 118 15 15 LYS HB3 H 1.940 0.020 2 119 15 15 LYS HG2 H 1.480 0.020 1 120 15 15 LYS HG3 H 1.480 0.020 1 121 15 15 LYS HD2 H 1.550 0.020 2 122 15 15 LYS HD3 H 1.570 0.020 2 123 15 15 LYS HE2 H 2.980 0.020 1 124 15 15 LYS HE3 H 2.980 0.020 1 125 16 16 ARG H H 7.810 0.020 1 126 16 16 ARG HA H 4.280 0.020 1 127 16 16 ARG HB2 H 1.860 0.020 2 128 16 16 ARG HB3 H 1.980 0.020 2 129 16 16 ARG HG2 H 1.710 0.020 1 130 16 16 ARG HG3 H 1.710 0.020 1 131 16 16 ARG HD2 H 3.210 0.020 1 132 16 16 ARG HD3 H 3.210 0.020 1 133 16 16 ARG HE H 7.470 0.020 1 134 17 17 LEU H H 7.750 0.020 1 135 17 17 LEU HA H 4.290 0.020 1 136 17 17 LEU HB2 H 1.730 0.020 2 137 17 17 LEU HB3 H 1.760 0.020 2 138 17 17 LEU HG H 1.640 0.020 1 139 17 17 LEU HD1 H 0.830 0.020 2 140 17 17 LEU HD2 H 0.920 0.020 2 141 17 17 LEU N N 119.380 0.500 1 142 18 18 GLY H H 7.590 0.020 1 143 18 18 GLY HA2 H 3.720 0.020 2 144 18 18 GLY HA3 H 3.760 0.020 2 stop_ save_