data_6020 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure-activity relationships for the beta-hairpin cationic antimicrobial peptide polyphemusin I ; _BMRB_accession_number 6020 _BMRB_flat_file_name bmr6020.str _Entry_type original _Submission_date 2003-11-21 _Accession_date 2003-11-24 _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 Powers Jon-Paul S. . 2 Rozek Annett . . 3 Hancock Robert E.W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 133 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-16 update BMRB 'Updating non-standard residue' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure-activity relationships for the beta-hairpin cationic antimicrobial peptide polyphemusin I ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15134657 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Powers Jon-Paul S. . 2 Rozek Annett . . 3 Hancock Robert E.W. . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_volume 1698 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 239 _Page_last 250 _Year 2004 _Details . save_ ################################## # Molecular system description # ################################## save_system_PM1 _Saveframe_category molecular_system _Mol_system_name 'Polyphemusin I' _Abbreviation_common PM1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'polyphemusin I' $Polyphemusin_I stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' loop_ _Biological_function 'antimicrobial peptide' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Polyphemusin_I _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Polyphemusin I' _Abbreviation_common PM1 _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence RRWCFRVCYRGFCYRKCRX loop_ _Residue_seq_code _Residue_label 1 ARG 2 ARG 3 TRP 4 CYS 5 PHE 6 ARG 7 VAL 8 CYS 9 TYR 10 ARG 11 GLY 12 PHE 13 CYS 14 TYR 15 ARG 16 LYS 17 CYS 18 ARG 19 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 1RKK "Polyphemusin I Nmr Solution Structure" 94.44 19 100.00 100.00 1.03e-01 SP P14215 "RecName: Full=Polyphemusin-1; AltName: Full=Polyphemusin I [Limulus polyphemus]" 94.44 18 100.00 100.00 1.05e-01 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'AMINO GROUP' _BMRB_code . _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 8 16:28:00 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? stop_ save_ ############# # Ligands # ############# save_NH2 _Saveframe_category ligand _Mol_type non-polymer _Name_common NH2 _Molecular_mass . _Details . _Mol_thiol_state . _Sequence_homology_query_date . save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single disulfide 'polyphemusin I' 4 CYS SG 'polyphemusin I' 17 CYS SG single disulfide 'polyphemusin I' 4 CYS SG 'polyphemusin I' 17 CYS SG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Organ _Cell_type $Polyphemusin_I 'Horseshoe crab' 61202 Eukaryota Metazoa Tachypleus polyphemus haemolymph haemocyte 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 $Polyphemusin_I 'chemical synthesis' . . . . . 'Synthesized by FMOC solid-phase 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 $Polyphemusin_I 2 mM . stop_ save_ ############################ # Computer software used # ############################ save_NMRView _Saveframe_category software _Name NMRView _Version 5.0.3 loop_ _Task 'Integration of NOESY peak volumes.' stop_ _Details ; B.A. Johnson, R.A. Blevins, NMRView: A computer program for the visualization and analysis of NMR data, J Biomol NMR 4 (1994) 603-614. ; save_ save_XPLOR-NIH _Saveframe_category software _Name XPLOR-NIH _Version 2.9.0 loop_ _Task 'Distance geometry simulated annealing' stop_ _Details ; C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clore, The Xplor-NIH NMR Molecular Structure Determination Package, J Magn Res 160 (2003) 66-74. ; save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H NOESY' _Sample_label $sample_1 save_ save_1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H TOCSY' _Sample_label $sample_1 save_ save_1H_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H DQF-COSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_Condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.0 0.2 n/a temperature 300 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 0.0 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_Shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'polyphemusin I' _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 ARG HA H 4.063 . . 2 . 1 ARG HB2 H 1.889 . 1 3 . 1 ARG HB3 H 1.889 . 1 4 . 1 ARG HG2 H 1.531 . 1 5 . 1 ARG HG3 H 1.531 . 1 6 . 1 ARG HD2 H 3.081 . 1 7 . 1 ARG HD3 H 3.081 . 1 8 . 1 ARG HE H 6.941 . . 9 . 2 ARG H H 8.735 . . 10 . 2 ARG HA H 4.725 . . 11 . 2 ARG HB2 H 1.766 . 1 12 . 2 ARG HB3 H 1.766 . 1 13 . 2 ARG HG2 H 1.602 . . 14 . 2 ARG HG3 H 1.660 . . 15 . 2 ARG HD2 H 3.172 . 1 16 . 2 ARG HD3 H 3.172 . 1 17 . 2 ARG HE H 7.163 . . 18 . 3 TRP H H 8.854 . . 19 . 3 TRP HA H 4.920 . . 20 . 3 TRP HB2 H 3.285 . . 21 . 3 TRP HB3 H 3.367 . . 22 . 3 TRP HD1 H 7.278 . . 23 . 3 TRP HE1 H 10.141 . . 24 . 3 TRP HE3 H 7.458 . . 25 . 3 TRP HZ2 H 7.686 . . 26 . 3 TRP HZ3 H 7.183 . 3 27 . 3 TRP HH2 H 7.132 . 3 28 . 4 CYS H H 8.349 . . 29 . 4 CYS HA H 5.565 . . 30 . 4 CYS HB2 H 2.582 . . 31 . 4 CYS HB3 H 3.025 . . 32 . 5 PHE H H 8.821 . . 33 . 5 PHE HA H 4.835 . . 34 . 5 PHE HB2 H 3.071 . . 35 . 5 PHE HB3 H 3.083 . . 36 . 5 PHE HD1 H 6.931 . 1 37 . 5 PHE HD2 H 6.931 . 1 38 . 5 PHE HE1 H 7.118 . 1 39 . 5 PHE HE2 H 7.118 . 1 40 . 5 PHE HZ H 7.107 . . 41 . 6 ARG H H 8.620 . . 42 . 6 ARG HA H 4.846 . . 43 . 6 ARG HB2 H 1.638 . . 44 . 6 ARG HB3 H 1.756 . . 45 . 6 ARG HG2 H 1.415 . . 46 . 6 ARG HG3 H 1.471 . . 47 . 6 ARG HD2 H 3.124 . 1 48 . 6 ARG HD3 H 3.124 . 1 49 . 6 ARG HE H 7.201 . . 50 . 7 VAL H H 8.859 . . 51 . 7 VAL HA H 4.327 . . 52 . 7 VAL HB H 1.515 . . 53 . 7 VAL HG1 H 0.820 . . 54 . 7 VAL HG2 H 0.889 . . 55 . 8 CYS H H 8.597 . . 56 . 8 CYS HA H 5.658 . . 57 . 8 CYS HB2 H 2.764 . . 58 . 8 CYS HB3 H 3.021 . . 59 . 9 TYR H H 9.251 . . 60 . 9 TYR HA H 4.799 . . 61 . 9 TYR HB2 H 3.141 . 1 62 . 9 TYR HB3 H 3.141 . 1 63 . 9 TYR HD1 H 7.295 . 1 64 . 9 TYR HD2 H 7.295 . 1 65 . 9 TYR HE1 H 6.906 . 1 66 . 9 TYR HE2 H 6.906 . 1 67 . 10 ARG H H 9.282 . . 68 . 10 ARG HA H 3.757 . . 69 . 10 ARG HB2 H 1.671 . . 70 . 10 ARG HB3 H 1.985 . . 71 . 10 ARG HG2 H 0.944 . . 72 . 10 ARG HG3 H 1.269 . . 73 . 10 ARG HD2 H 3.104 . 1 74 . 10 ARG HD3 H 3.104 . 1 75 . 10 ARG HE H 7.071 . . 76 . 11 GLY H H 8.592 . . 77 . 11 GLY HA2 H 3.583 . . 78 . 11 GLY HA3 H 4.153 . . 79 . 12 PHE H H 7.994 . . 80 . 12 PHE HA H 4.909 . . 81 . 12 PHE HB2 H 3.149 . . 82 . 12 PHE HB3 H 3.241 . . 83 . 12 PHE HD1 H 7.359 . 1 84 . 12 PHE HD2 H 7.359 . 1 85 . 12 PHE HE1 H 7.882 . 1 86 . 12 PHE HE2 H 7.882 . 1 87 . 13 CYS H H 8.409 . . 88 . 13 CYS HA H 5.803 . . 89 . 13 CYS HB2 H 2.547 . . 90 . 13 CYS HB3 H 2.937 . . 91 . 14 TYR H H 9.053 . . 92 . 14 TYR HA H 4.746 . . 93 . 14 TYR HB2 H 2.989 . 1 94 . 14 TYR HB3 H 2.989 . 1 95 . 14 TYR HD1 H 6.972 . 1 96 . 14 TYR HD2 H 6.972 . 1 97 . 14 TYR HE1 H 6.756 . 1 98 . 14 TYR HE2 H 6.756 . 1 99 . 15 ARG H H 8.580 . . 100 . 15 ARG HA H 4.758 . . 101 . 15 ARG HB2 H 1.680 . 1 102 . 15 ARG HB3 H 1.680 . 1 103 . 15 ARG HG2 H 1.368 . . 104 . 15 ARG HG3 H 1.476 . . 105 . 15 ARG HD2 H 3.116 . 1 106 . 15 ARG HD3 H 3.116 . 1 107 . 15 ARG HE H 7.198 . . 108 . 16 LYS H H 8.796 . . 109 . 16 LYS HA H 4.565 . . 110 . 16 LYS HB2 H 1.300 . . 111 . 16 LYS HB3 H 1.441 . . 112 . 16 LYS HG2 H 1.342 . 1 113 . 16 LYS HG3 H 1.342 . 1 114 . 16 LYS HD2 H 1.768 . 1 115 . 16 LYS HD3 H 1.768 . 1 116 . 16 LYS HE2 H 3.032 . 1 117 . 16 LYS HE3 H 3.032 . 1 118 . 16 LYS HZ H 7.670 . . 119 . 17 CYS H H 8.676 . . 120 . 17 CYS HA H 5.524 . . 121 . 17 CYS HB2 H 2.813 . . 122 . 17 CYS HB3 H 2.993 . . 123 . 18 ARG H H 8.952 . . 124 . 18 ARG HA H 4.579 . . 125 . 18 ARG HB2 H 1.829 . . 126 . 18 ARG HB3 H 1.999 . . 127 . 18 ARG HG2 H 1.783 . 1 128 . 18 ARG HG3 H 1.783 . 1 129 . 18 ARG HD2 H 3.246 . 1 130 . 18 ARG HD3 H 3.246 . 1 131 . 18 ARG HE H 7.238 . . 132 . 19 NH2 HN1 H 7.882 . 1 133 . 19 NH2 HN2 H 7.882 . 1 stop_ save_