data_20125 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DPC micelle bound VK22 ; _BMRB_accession_number 20125 _BMRB_flat_file_name bmr20125.str _Entry_type new _Submission_date 2010-07-05 _Accession_date 2010-07-05 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Deletion analogue of chicken antimicrobial peptide Fowlicidin1 VK22 in DPC micelle bound form. Oligomeric structure of the antimicrobial peptide.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bhattacharjya Surajit . . 2 Saravanan Rathi . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 96 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-02-03 update BMRB 'update entry citation' 2010-11-05 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 20100 'VK22 in LPS micelle' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Oligomeric structure of a cathelicidin antimicrobial peptide in dodecylphosphocholine micelle determined by NMR spectroscopy.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20933496 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Saravanan Rathi . . 2 Bhattacharjya Surajit . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et biophysica acta' _Journal_volume 1808 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 369 _Page_last 381 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'VK22 in DPC micelles' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DPCmicelle bound VK22 chain A' $VK22 'DPCmicelle bound VK22 chain B' $VK22 'DPCmicelle bound VK22 chain C' $VK22 'DPCmicelle bound VK22 chain D' $VK22 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details Tetramer save_ ######################## # Monomeric polymers # ######################## save_VK22 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common VK22 _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'antimicrobial peptide' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; VWPLVIRTVIAGYNLYRAIK KK ; loop_ _Residue_seq_code _Residue_label 1 VAL 2 TRP 3 PRO 4 LEU 5 VAL 6 ILE 7 ARG 8 THR 9 VAL 10 ILE 11 ALA 12 GLY 13 TYR 14 ASN 15 LEU 16 TYR 17 ARG 18 ALA 19 ILE 20 LYS 21 LYS 22 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 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 15667 LK19 86.36 19 100.00 100.00 2.88e-02 BMRB 15979 Fowlicidin-1 86.36 19 100.00 100.00 2.88e-02 BMRB 21013 RI23 86.36 23 100.00 100.00 4.30e-03 PDB 2AMN "Solution Structure Of Fowlicidin-1, A Novel Cathelicidin Antimicrobial Peptide From Chicken" 100.00 26 100.00 100.00 4.76e-05 DBJ BAF75952 "cathelicidin-1 [Gallus gallus]" 100.00 148 100.00 100.00 2.43e-06 GB AAS99323 "cathelicidin [Gallus gallus]" 100.00 148 100.00 100.00 2.43e-06 GB AAZ42399 "fowlicidin-1 [Gallus gallus]" 100.00 148 100.00 100.00 2.43e-06 GB AAZ65841 "fowlicidin-1 [Gallus gallus]" 100.00 148 100.00 100.00 2.16e-06 GB ACR22842 "fowlicidin-1 [Gallus gallus]" 100.00 148 100.00 100.00 2.43e-06 GB ADZ99028 "fowlicidin-1 [Gallus gallus]" 100.00 148 100.00 100.00 2.43e-06 REF NP_001001605 "cathelicidin-1 precursor [Gallus gallus]" 100.00 148 100.00 100.00 2.43e-06 SP Q6QLQ5 "RecName: Full=Cathelicidin-1; Short=CATH-1; AltName: Full=Fowlicidin-1; Flags: Precursor" 100.00 148 100.00 100.00 2.43e-06 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $VK22 . . . . . . 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 $VK22 'recombinant technology' . . . . . 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 $VK22 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _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 _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 315 . K pH 4.8 . pH 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 DSS H 1 'methyl protons' ppm 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '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 'DPCmicelle bound VK22 chain A' _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 2 2 TRP HE1 H 10.712 0.000 3 2 2 2 TRP HZ2 H 7.471 0.021 3 3 2 2 TRP HZ3 H 7.086 0.000 3 4 3 3 PRO HB2 H 2.378 0.001 1 5 4 4 LEU H H 8.106 0.026 1 6 4 4 LEU HA H 3.652 0.000 1 7 4 4 LEU HB2 H 1.587 0.007 1 8 4 4 LEU HB3 H 1.587 0.007 1 9 4 4 LEU HG H 1.504 0.000 1 10 5 5 VAL H H 8.171 0.010 1 11 5 5 VAL HA H 3.665 0.015 1 12 5 5 VAL HB H 2.192 0.021 1 13 5 5 VAL HG1 H 0.905 0.000 1 14 5 5 VAL HG1 H 1.044 0.002 1 15 5 5 VAL HG1 H 0.905 0.000 1 16 6 6 ILE H H 7.597 0.005 1 17 6 6 ILE HA H 4.110 0.005 1 18 6 6 ILE HB H 1.994 0.007 1 19 6 6 ILE HD1 H 0.892 0.000 2 20 6 6 ILE HG2 H 1.600 0.001 2 21 6 6 ILE HG2 H 1.197 0.000 2 22 7 7 ARG H H 8.088 0.002 1 23 7 7 ARG HA H 3.986 0.019 1 24 7 7 ARG HB2 H 1.965 0.008 2 25 7 7 ARG HB3 H 1.828 0.002 2 26 7 7 ARG HD2 H 3.223 0.000 1 27 7 7 ARG HD3 H 3.223 0.000 1 28 7 7 ARG HG2 H 1.718 0.000 1 29 7 7 ARG HG3 H 1.718 0.000 1 30 8 8 THR H H 7.990 0.013 1 31 8 8 THR HA H 4.296 0.009 1 32 8 8 THR HB H 3.854 0.008 1 33 8 8 THR HG2 H 1.163 0.002 2 34 9 9 VAL H H 8.089 0.001 1 35 9 9 VAL HA H 3.639 0.003 1 36 9 9 VAL HB H 2.216 0.003 1 37 9 9 VAL HG1 H 0.910 0.004 2 38 9 9 VAL HG1 H 1.050 0.004 2 39 9 9 VAL HG1 H 0.910 0.004 2 40 10 10 ILE H H 8.178 0.001 1 41 10 10 ILE HB H 1.897 0.006 1 42 10 10 ILE HD1 H 0.812 0.000 2 43 10 10 ILE HG12 H 0.985 0.004 2 44 10 10 ILE HG2 H 1.817 0.003 2 45 11 11 ALA H H 8.037 0.003 1 46 11 11 ALA HA H 4.301 0.006 1 47 11 11 ALA HB H 1.602 0.001 1 48 12 12 GLY H H 8.785 0.002 1 49 12 12 GLY HA2 H 3.781 0.003 1 50 12 12 GLY HA3 H 3.649 0.013 1 51 13 13 TYR H H 8.769 0.029 1 52 13 13 TYR HA H 4.259 0.007 1 53 13 13 TYR HB2 H 3.285 0.005 2 54 13 13 TYR HB3 H 3.033 0.015 2 55 13 13 TYR HD1 H 7.014 0.003 2 56 14 14 ASN H H 8.585 0.001 1 57 14 14 ASN HA H 4.408 0.215 1 58 14 14 ASN HB2 H 3.004 0.001 2 59 14 14 ASN HB3 H 2.734 0.002 2 60 15 15 LEU H H 8.245 0.002 1 61 15 15 LEU HA H 4.181 0.001 1 62 15 15 LEU HB2 H 1.907 0.004 1 63 15 15 LEU HB3 H 1.823 0.000 1 64 15 15 LEU HD1 H 0.956 0.016 2 65 15 15 LEU HD2 H 0.956 0.016 2 66 16 16 TYR H H 8.362 0.002 1 67 16 16 TYR HA H 3.972 0.003 1 68 16 16 TYR HB2 H 3.275 0.002 2 69 16 16 TYR HB3 H 3.014 0.002 2 70 16 16 TYR HD1 H 6.820 0.002 2 71 16 16 TYR HE1 H 6.767 0.022 1 72 17 17 ARG H H 8.183 0.065 1 73 17 17 ARG HA H 3.590 0.101 1 74 17 17 ARG HB2 H 1.806 0.103 1 75 17 17 ARG HB3 H 1.488 0.009 1 76 17 17 ARG HG2 H 1.526 0.208 2 77 17 17 ARG HG3 H 1.526 0.208 2 78 18 18 ALA H H 7.631 0.001 1 79 18 18 ALA HA H 4.124 0.000 1 80 18 18 ALA HB H 1.508 0.000 1 81 19 19 ILE H H 7.800 0.002 1 82 19 19 ILE HA H 3.895 0.001 1 83 19 19 ILE HB H 1.846 0.001 1 84 19 19 ILE HD1 H 0.871 0.002 2 85 19 19 ILE HG2 H 1.647 0.000 2 86 19 19 ILE HG2 H 1.285 0.045 2 87 20 20 LYS H H 7.728 0.002 1 88 20 20 LYS HA H 4.087 0.001 1 89 20 20 LYS HB2 H 1.823 0.000 1 90 20 20 LYS HG2 H 1.428 0.009 2 91 20 20 LYS HG3 H 1.428 0.009 2 92 21 21 LYS H H 7.632 0.002 1 93 21 21 LYS HA H 4.174 0.000 1 94 21 21 LYS HB2 H 1.842 0.000 1 95 22 22 LYS H H 7.742 0.000 1 96 22 22 LYS HA H 4.133 0.000 1 stop_ save_