data_18418 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Pleurocidin-NH2 ; _BMRB_accession_number 18418 _BMRB_flat_file_name bmr18418.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 Kozlowska Justyna . . 3 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" 120 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-04-01 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 18420 Magainin stop_ _Original_release_date 2013-04-01 save_ ############################# # Citation for this entry # ############################# save_MD_paper_LSV _Saveframe_category entry_citation _Citation_full . _Citation_title 'All Atom Simulations of the Initial Binding of Magainin and Pleurocidin to Membranes Comprising of 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 pleurocidin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label pleurocidin $pleurocidin 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_pleurocidin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common pleurocidin _Molecular_mass 2718.215 _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; GWGSFFKKAAHVGKHVGKAA LTHYL ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 TRP 3 3 GLY 4 4 SER 5 5 PHE 6 6 PHE 7 7 LYS 8 8 LYS 9 9 ALA 10 10 ALA 11 11 HIS 12 12 VAL 13 13 GLY 14 14 LYS 15 15 HIS 16 16 VAL 17 17 GLY 18 18 LYS 19 19 ALA 20 20 ALA 21 21 LEU 22 22 THR 23 23 HIS 24 24 TYR 25 25 LEU 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 1Z64 "Nmr Solution Structure Of Pleurocidin In Dpc Micelles" 100.00 26 100.00 100.00 2.91e-07 PDB 2LS9 Pleurocidin-nh2 100.00 25 100.00 100.00 2.90e-07 GB AAF17252 "antimicrobial peptide pleurocidin [Pseudopleuronectes americanus]" 100.00 68 100.00 100.00 5.77e-08 GB AAF17253 "antimicrobial peptide pleurocidin [Pseudopleuronectes americanus]" 100.00 68 100.00 100.00 5.77e-08 GB AAG10397 "pleurocidin 2 prepropolypeptide [Pseudopleuronectes americanus]" 100.00 68 100.00 100.00 5.77e-08 GB AAK52842 "pleurocidin prepropolypeptide, partial [Pseudopleuronectes americanus]" 100.00 60 100.00 100.00 7.42e-08 GB AAK52846 "pleurocidin prepropolypeptide, partial [Pseudopleuronectes americanus]" 100.00 60 100.00 100.00 7.42e-08 SP P81941 "RecName: Full=Pleurocidin; Flags: Precursor [Pseudopleuronectes americanus]" 100.00 68 100.00 100.00 5.77e-08 SP Q90ZY0 "RecName: Full=Pleurocidin; Flags: Precursor [Pseudopleuronectes americanus]" 100.00 68 100.00 100.00 6.02e-08 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $pleurocidin . . . . . . 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 $pleurocidin 'chemical synthesis' . . . . . 'Amidated C-terminus' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'pH 7.0' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling TRIS 5 mM 'natural abundance' $pleurocidin 1 mM 'natural abundance' SDS 100 mM [U-2H] TSP 0.05 % 'natural abundance' 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_ARIA _Saveframe_category software _Name ARIA _Version . loop_ _Vendor _Address _Electronic_address 'Linge, O'Donoghue and Nilges' . . stop_ loop_ _Task 'structure solution' refinement 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_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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _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 7.0 . pH pressure 1 . atm 'ionic strength' 5 . 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 pleurocidin _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 4.249 0.000 1 2 1 1 GLY HA3 H 4.249 0.000 1 3 2 2 TRP H H 8.575 0.006 1 4 2 2 TRP HA H 4.595 0.004 1 5 3 3 GLY H H 8.113 0.006 1 6 3 3 GLY HA2 H 4.096 0.133 1 7 3 3 GLY HA3 H 4.096 0.133 1 8 4 4 SER H H 8.490 0.174 1 9 4 4 SER HA H 4.803 0.006 1 10 4 4 SER HB2 H 3.984 0.076 1 11 4 4 SER HB3 H 3.984 0.076 1 12 5 5 PHE H H 8.067 0.006 1 13 5 5 PHE HA H 4.284 0.015 1 14 5 5 PHE HB2 H 3.179 0.099 1 15 5 5 PHE HB3 H 3.179 0.099 1 16 6 6 PHE H H 8.306 0.009 1 17 6 6 PHE HA H 4.183 0.012 1 18 6 6 PHE HB2 H 3.266 0.002 1 19 6 6 PHE HB3 H 3.266 0.002 1 20 7 7 LYS H H 8.100 0.003 1 21 7 7 LYS HA H 4.028 0.007 1 22 7 7 LYS HB2 H 1.894 0.098 1 23 7 7 LYS HB3 H 1.894 0.098 1 24 7 7 LYS HG2 H 1.510 0.004 1 25 7 7 LYS HG3 H 1.510 0.004 1 26 7 7 LYS HD2 H 1.701 0.011 1 27 7 7 LYS HD3 H 1.701 0.011 1 28 7 7 LYS HE2 H 3.016 0.001 1 29 7 7 LYS HE3 H 3.016 0.001 1 30 8 8 LYS H H 7.734 0.003 1 31 8 8 LYS HA H 4.159 0.012 1 32 8 8 LYS HB2 H 1.830 0.110 1 33 8 8 LYS HB3 H 1.830 0.110 1 34 8 8 LYS HG2 H 1.505 0.012 1 35 8 8 LYS HG3 H 1.505 0.012 1 36 8 8 LYS HD2 H 1.622 0.006 1 37 8 8 LYS HD3 H 1.622 0.006 1 38 8 8 LYS HE2 H 2.984 0.005 1 39 8 8 LYS HE3 H 2.984 0.005 1 40 9 9 ALA H H 8.328 0.005 1 41 9 9 ALA HA H 3.970 0.011 1 42 9 9 ALA HB H 1.280 0.007 1 43 10 10 ALA H H 8.295 0.009 1 44 10 10 ALA HA H 3.988 0.003 1 45 10 10 ALA HB H 1.503 0.001 1 46 11 11 HIS H H 7.890 0.003 1 47 11 11 HIS HA H 4.415 0.004 1 48 11 11 HIS HB2 H 3.911 1.408 1 49 11 11 HIS HB3 H 3.911 1.408 1 50 11 11 HIS HD2 H 8.261 0.000 1 51 11 11 HIS HE1 H 7.211 0.001 1 52 12 12 VAL H H 8.154 0.003 1 53 12 12 VAL HA H 3.848 0.006 1 54 12 12 VAL HB H 2.236 0.005 1 55 12 12 VAL HG1 H 1.084 0.060 1 56 12 12 VAL HG2 H 1.084 0.060 1 57 13 13 GLY H H 8.869 0.003 1 58 13 13 GLY HA3 H 3.714 0.001 1 59 14 14 LYS H H 8.321 0.006 1 60 14 14 LYS HA H 4.002 0.010 1 61 14 14 LYS HB2 H 1.930 0.012 1 62 14 14 LYS HB3 H 1.930 0.012 1 63 14 14 LYS HG2 H 1.509 0.000 1 64 14 14 LYS HG3 H 1.509 0.000 1 65 14 14 LYS HD2 H 1.559 0.000 1 66 14 14 LYS HD3 H 1.559 0.000 1 67 14 14 LYS HE2 H 2.966 0.000 1 68 14 14 LYS HE3 H 2.966 0.000 1 69 15 15 HIS H H 7.749 0.005 1 70 15 15 HIS HA H 4.413 0.001 1 71 15 15 HIS HB2 H 3.330 0.046 1 72 15 15 HIS HB3 H 3.330 0.046 1 73 16 16 VAL H H 8.540 0.007 1 74 16 16 VAL HA H 3.829 0.008 1 75 16 16 VAL HB H 2.222 0.005 1 76 16 16 VAL HG1 H 1.073 0.055 1 77 16 16 VAL HG2 H 1.073 0.055 1 78 17 17 GLY H H 8.711 0.002 1 79 17 17 GLY HA3 H 3.762 0.000 1 80 18 18 LYS H H 8.312 0.007 1 81 18 18 LYS HA H 4.065 0.061 1 82 18 18 LYS HB2 H 1.961 0.000 1 83 18 18 LYS HB3 H 1.961 0.000 1 84 18 18 LYS HG2 H 1.510 0.000 1 85 18 18 LYS HG3 H 1.510 0.000 1 86 18 18 LYS HD2 H 1.749 0.008 1 87 18 18 LYS HD3 H 1.749 0.008 1 88 19 19 ALA H H 7.968 0.001 1 89 19 19 ALA HA H 4.215 0.004 1 90 19 19 ALA HB H 1.559 0.001 1 91 20 20 ALA H H 8.562 0.003 1 92 20 20 ALA HA H 4.162 0.005 1 93 20 20 ALA HB H 1.606 0.002 1 94 21 21 LEU H H 8.437 0.009 1 95 21 21 LEU HA H 4.175 0.004 1 96 21 21 LEU HB2 H 1.885 0.002 1 97 21 21 LEU HB3 H 1.885 0.002 1 98 21 21 LEU HG H 0.994 0.001 1 99 22 22 THR H H 8.338 0.007 1 100 22 22 THR HA H 3.960 0.005 1 101 22 22 THR HB H 4.331 0.007 1 102 22 22 THR HG2 H 1.297 0.006 1 103 23 23 HIS H H 8.067 0.006 1 104 23 23 HIS HA H 4.333 0.005 1 105 23 23 HIS HE1 H 7.208 0.000 1 106 24 24 TYR H H 8.333 0.007 1 107 24 24 TYR HA H 4.306 0.004 1 108 24 24 TYR HB2 H 3.110 0.041 1 109 24 24 TYR HB3 H 3.110 0.041 1 110 24 24 TYR HD1 H 7.207 0.002 1 111 24 24 TYR HD2 H 7.207 0.002 1 112 24 24 TYR HE1 H 6.855 0.000 1 113 24 24 TYR HE2 H 6.855 0.000 1 114 25 25 LEU H H 8.262 0.003 1 115 25 25 LEU HA H 4.215 0.004 1 116 25 25 LEU HB2 H 1.891 0.007 1 117 25 25 LEU HB3 H 1.891 0.007 1 118 25 25 LEU HG H 1.635 0.003 1 119 25 25 LEU HD1 H 0.986 0.003 1 120 25 25 LEU HD2 H 0.986 0.003 1 stop_ save_