data_6168 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structures of antimicrobial hexapeptides bound to DPC micelles ; _BMRB_accession_number 6168 _BMRB_flat_file_name bmr6168.str _Entry_type original _Submission_date 2004-04-02 _Accession_date 2004-04-02 _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 Appelt C. . . 2 Soderhall J. A. . 3 Bienert M. . . 4 Dathe M. . . 5 Schmieder P. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 52 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-17 update BMRB 'Updating non-standard residue' stop_ loop_ _Related_BMRB_accession_number _Relationship 6169 'cyclic hexapeptide KKWWKF' 6170 'cyclic hexapeptide RRYYRF' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of the Antimicrobial, Cationic Hexapeptide Cyclo(RRWWRF) and Its Analogues in Solution and Bound to Detergent Micelles' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16075425 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Appelt C. . . 2 Wessolowski A. . . 3 Soderhall J. A. . 4 Dathe M. . . 5 Schmieder P. . . stop_ _Journal_abbreviation ChemBioChem _Journal_volume 6 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1654 _Page_last 1662 _Year 2005 _Details . loop_ _Keyword 'antimicrobial peptide' 'cyclic peptide' stop_ save_ ################################## # Molecular system description # ################################## save_system_cyclic_hexapeptide _Saveframe_category molecular_system _Mol_system_name 'cyclic hexapeptide RR(NAL)(NAL)RF' _Abbreviation_common 'cyclic hexapeptide RR(NAL)(NAL)RF' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'cyclic hexapeptide RR(NAL)(NAL)RF' $cyclic_hexapeptide stop_ _System_molecular_weight . _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_cyclic_hexapeptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'cyclic hexapeptide RR(NAL)(NAL)RF' _Abbreviation_common 'cyclic hexapeptide RR(NAL)(NAL)RF' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 6 _Mol_residue_sequence RRXXRF loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ARG 2 2 ARG 3 3 NAL 4 4 NAL 5 5 ARG 6 6 PHE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NAL _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common BETA-(2-NAPHTHYL)-ALANINE _BMRB_code . _PDB_code NAL _Standard_residue_derivative . _Molecular_mass 215.248 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 3 16:20:16 2012 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C4A C4A C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C8A C8A C . 0 . ? C9 C9 C . 0 . ? CA CA C . 0 . ? C C C . 0 . ? N N N . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H1 H1 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H91 H91 H . 0 . ? H92 H92 H . 0 . ? HA HA H . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HXT HXT 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 DOUB C6 C5 ? ? SING C6 C7 ? ? SING C5 C4A ? ? DOUB C7 C8 ? ? DOUB C4A C4 ? ? SING C4A C8A ? ? SING C8 C8A ? ? SING C4 C3 ? ? DOUB C8A C1 ? ? DOUB C3 C2 ? ? SING C1 C2 ? ? SING C2 C9 ? ? SING C9 CA ? ? SING CA N ? ? SING CA C ? ? DOUB C O ? ? SING C OXT ? ? SING C1 H1 ? ? SING C3 H3 ? ? SING C4 H4 ? ? SING C5 H5 ? ? SING C6 H6 ? ? SING C7 H7 ? ? SING C8 H8 ? ? SING C9 H91 ? ? SING C9 H92 ? ? SING CA HA ? ? SING N H ? ? SING N H2 ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $cyclic_hexapeptide . . . . . . 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 $cyclic_hexapeptide 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelles _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $cyclic_hexapeptide 2.5 mM . 'D38 dodecyl phosphocholine' 50 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 2.6 loop_ _Task collection stop_ _Details Bruker save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.1 loop_ _Task 'data analysis' stop_ _Details 'Goddard, T.D. and Kneller, D.G.' save_ save_AMBER _Saveframe_category software _Name AMBER _Version 6 loop_ _Task 'structure solution, refinement' stop_ _Details 'Case, D.A. et al' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.3 . pH pressure 1 . atm temperature 300 . 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 . H 1 . ppm . . . . . . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'cyclic hexapeptide RR(NAL)(NAL)RF' _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 ARG HA H 4.093 0.004 1 2 1 1 ARG HB2 H 1.888 0.007 2 3 1 1 ARG HB3 H 1.836 0.009 2 4 1 1 ARG HD2 H 3.197 0.002 1 5 1 1 ARG HD3 H 3.197 0.002 1 6 1 1 ARG HE H 7.525 0.002 1 7 1 1 ARG HG2 H 1.578 0.003 1 8 1 1 ARG HG3 H 1.578 0.003 1 9 1 1 ARG H H 8.646 0.001 1 10 2 2 ARG HA H 4.146 0.003 1 11 2 2 ARG HB2 H 1.622 0.003 1 12 2 2 ARG HB3 H 1.713 0.003 1 13 2 2 ARG HD2 H 2.977 0.002 2 14 2 2 ARG HD3 H 2.877 0.003 2 15 2 2 ARG HE H 7.414 0.001 1 16 2 2 ARG HG2 H 1.406 0.003 2 17 2 2 ARG HG3 H 1.265 0.003 2 18 2 2 ARG H H 8.565 0.001 1 19 3 3 NAL H3 H 4.742 0.002 1 20 3 3 NAL H4 H 3.360 0.003 2 21 3 3 NAL H5 H 3.219 0.003 2 22 3 3 NAL H6 H 7.358 0.004 1 23 3 3 NAL H7 H 7.640 0.003 1 24 3 3 NAL H1 H 7.547 0.004 1 25 4 4 NAL H3 H 4.633 0.003 1 26 4 4 NAL H4 H 3.318 0.002 2 27 4 4 NAL H5 H 3.220 0.003 2 28 4 4 NAL H6 H 7.467 0.014 1 29 4 4 NAL H7 H 7.549 0.003 1 30 4 4 NAL H8 H 7.882 0.009 1 31 4 4 NAL H91 H 7.849 0.004 1 32 4 4 NAL H92 H 7.437 0.002 1 33 4 4 NAL H1 H 9.022 0.003 1 34 4 4 NAL HXT H 7.430 0.003 1 35 5 5 ARG HA H 3.991 0.002 1 36 5 5 ARG HB2 H 1.598 0.003 2 37 5 5 ARG HB3 H 1.020 0.004 2 38 5 5 ARG HD2 H 2.694 0.005 2 39 5 5 ARG HD3 H 2.406 0.007 2 40 5 5 ARG HE H 7.083 0.002 1 41 5 5 ARG HG2 H 0.775 0.009 2 42 5 5 ARG HG3 H 0.466 0.007 2 43 5 5 ARG H H 7.221 0.004 1 44 6 6 PHE HA H 4.743 0.005 1 45 6 6 PHE HB2 H 2.984 0.003 1 46 6 6 PHE HB3 H 3.534 0.003 1 47 6 6 PHE HD1 H 7.128 0.003 1 48 6 6 PHE HD2 H 7.128 0.003 1 49 6 6 PHE HE1 H 7.260 0.006 1 50 6 6 PHE HE2 H 7.260 0.006 1 51 6 6 PHE H H 8.148 0.002 1 52 6 6 PHE HZ H 7.253 0.002 1 stop_ save_