data_18420 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; magainin ; _BMRB_accession_number 18420 _BMRB_flat_file_name bmr18420.str _Entry_type original _Submission_date 2012-04-24 _Accession_date 2012-04-24 _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 Vermeer Louic S. . 2 Mason James A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 53 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-04-01 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 18418 Pleurocidin stop_ _Original_release_date 2013-04-01 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'All Atom Simulations of the Initial Binding of Magainin and Pleurocidin to Membranes Comprising a Mixture of Anionic and Zwitterionic Lipids' _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 Vermeer Louic S. . 2 Kozlowska Justyna . . 3 Lorenz Chris D. . 4 Mason James A. . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _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 magainin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label magainin $magainin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_magainin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common magainin _Molecular_mass 2471.959 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 23 _Mol_residue_sequence ; GIGKFLHSAKKFGKAFVGEI MNS ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 GLY 4 LYS 5 PHE 6 LEU 7 HIS 8 SER 9 ALA 10 LYS 11 LYS 12 PHE 13 GLY 14 LYS 15 ALA 16 PHE 17 VAL 18 GLY 19 GLU 20 ILE 21 MET 22 ASN 23 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 2LSA Magainin 100.00 23 100.00 100.00 1.09e-05 PDB 2MAG "Nmr Structure Of Magainin 2 In Dpc Micelles, 10 Structures" 100.00 24 100.00 100.00 1.09e-05 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $magainin 'African clawed frog' 8355 Eukaryota Metazoa Xenopus laevis 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 $magainin 'chemical 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 $magainin 1 mM 'natural abundance' TRIS 5 mM 'natural abundance' TSP 0.05 % 'natural abundance' SDS 100 mM [U-2H] H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_AQUA _Saveframe_category software _Name AQUA _Version . loop_ _Vendor _Address _Electronic_address 'Rullmann, Doreleijers and Kaptein' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_ARIA _Saveframe_category software _Name ARIA _Version . loop_ _Vendor _Address _Electronic_address 'Linge, O'Donoghue and Nilges' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.2 . pH pressure 1 . atm 'ionic strength' 105 . mM stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 TSP H 1 'methyl protons' ppm 0 internal direct . . . 1 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 _Details . loop_ _Experiment_label '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 magainin _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 GLY HA2 H 3.777 0.007 2 2 1 1 GLY HA3 H 3.777 0.007 2 3 2 2 ILE H H 8.590 0.001 1 4 2 2 ILE HA H 4.269 0.001 1 5 3 3 GLY H H 8.591 0.000 1 6 3 3 GLY HA2 H 4.021 0.114 2 7 3 3 GLY HA3 H 4.021 0.114 2 8 4 4 LYS H H 7.854 0.008 1 9 4 4 LYS HA H 4.138 0.002 1 10 5 5 PHE H H 7.897 0.005 1 11 5 5 PHE HA H 4.501 0.001 1 12 6 6 LEU H H 8.056 0.002 1 13 6 6 LEU HA H 4.019 0.001 1 14 7 7 HIS H H 8.196 0.001 1 15 7 7 HIS HA H 4.397 0.001 1 16 8 8 SER H H 8.022 0.001 1 17 8 8 SER HA H 4.343 0.003 1 18 8 8 SER HB2 H 4.044 0.044 2 19 8 8 SER HB3 H 4.044 0.044 2 20 9 9 ALA H H 8.367 0.001 1 21 9 9 ALA HA H 4.083 0.001 1 22 10 10 LYS H H 8.089 0.002 1 23 10 10 LYS HA H 3.964 0.007 1 24 11 11 LYS H H 7.659 0.004 1 25 11 11 LYS HA H 4.024 0.001 1 26 12 12 PHE H H 8.196 0.003 1 27 12 12 PHE HA H 4.459 0.001 1 28 13 13 GLY H H 8.713 0.003 1 29 13 13 GLY HA2 H 3.824 0.001 2 30 13 13 GLY HA3 H 3.824 0.001 2 31 14 14 LYS H H 8.352 0.005 1 32 14 14 LYS HA H 4.002 0.001 1 33 15 15 ALA H H 7.747 0.002 1 34 15 15 ALA HA H 4.188 0.002 1 35 16 16 PHE H H 8.280 0.002 1 36 16 16 PHE HA H 4.298 0.001 1 37 17 17 VAL H H 8.249 0.012 1 38 17 17 VAL HA H 3.588 0.001 1 39 18 18 GLY H H 8.122 0.004 1 40 18 18 GLY HA2 H 3.870 0.050 2 41 18 18 GLY HA3 H 3.870 0.050 2 42 19 19 GLU H H 7.731 0.007 1 43 19 19 GLU HA H 4.224 0.000 1 44 20 20 ILE H H 7.696 0.003 1 45 20 20 ILE HA H 3.852 0.002 1 46 21 21 MET H H 8.168 0.001 1 47 21 21 MET HA H 4.315 0.000 1 48 22 22 ASN H H 7.905 0.001 1 49 22 22 ASN HA H 4.744 0.001 1 50 23 23 SER H H 7.947 0.001 1 51 23 23 SER HA H 4.186 0.194 1 52 23 23 SER HB2 H 3.961 0.000 2 53 23 23 SER HB3 H 3.961 0.000 2 stop_ save_