data_6411 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; FRAGMENT 33-61 OF BOVINE alpha-HEMOGLBIN: THE EFFECT OF C-TERMINAL AMIDATION AND IDENTIFICATION OF THE MINIMAL PORTION WITH ANTIFUNGAL ACTIVITY ; _BMRB_accession_number 6411 _BMRB_flat_file_name bmr6411.str _Entry_type original _Submission_date 2004-12-06 _Accession_date 2004-12-07 _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 Machado Alessandra . . 2 Sforca Mauricio L. . 3 Miranda Antonio . . 4 Daffre Sirlei . . 5 Spisni Alberto . . 6 Pertinhez Thelma A. . 7 Miranda 'M. Teresa' M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 62 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-16 update BMRB 'Updating non-standard residue' stop_ loop_ _Related_BMRB_accession_number _Relationship 6412 'Fragment 48-61 of bovine alpha-hemoglobin' 6413 'Fragment 40-61' 6414 'Amidated fragment 33-52' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The micelle-bound structure of an antimicrobial peptide derived from the alpha-chain of bovine hemoglobin isolated from the tick Boophilus microplus. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15850378 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sforca Mauricio L. . 2 Machado Alessandra . . 3 Figueredo Rita C. . 4 Oyama Sergio . Jr. 5 Silva Fernanda D. . 6 Miranda Antonio . . 7 Daffre Sirlei . . 8 Miranda M. Teresa . 9 Spisni Alberto . . 10 Pertinhez Thelma A. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 44 _Journal_issue 17 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6440 _Page_last 6451 _Year 2005 _Details . loop_ _Keyword 'antimicrobial peptide' 'MINIMAL PEPTIDE SEQUENCE' 'STRUCTURAL REQUIREMENTS' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full ; Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 1995, 6, 277-293; Johnson, B.; Blevins, R. A. NMRView: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR 1994, 4, 603-614. ; _Citation_title 'NMRPipe: a multidimensional spectral processing system based on UNIX pipes.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8520220 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Delaglio F. . . 2 Grzesiek S. . . 3 Vuister 'G. W.' W. . 4 Zhu G. . . 5 Pfeifer J. . . 6 Bax A. . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 3 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 277 _Page_last 293 _Year 1995 _Details ; The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks. ; save_ ################################## # Molecular system description # ################################## save_system_hb48-61a _Saveframe_category molecular_system _Mol_system_name 'amidated fragment 48-61 of bovine alpha-hemoglobin' _Abbreviation_common hb48-61a _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'amidated fragment 48-61' $48-61_amidated_fragment stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_48-61_amidated_fragment _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'amidated fragment 48-61' _Abbreviation_common 'amidated fragment 48-61' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence LSHGSAQVKGHGAKX loop_ _Residue_seq_code _Residue_label 1 LEU 2 SER 3 HIS 4 GLY 5 SER 6 ALA 7 GLN 8 VAL 9 LYS 10 GLY 11 HIS 12 GLY 13 ALA 14 LYS 15 NH2 stop_ _Sequence_homology_query_date 2005-11-24 _Sequence_homology_query_revised_last_date 2005-10-27 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 1 10:18:50 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_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $48-61_amidated_fragment Cow 9913 Eukaryota Metazoa Bos taurus 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 $48-61_amidated_fragment '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 _Concentration_max_value _Isotopic_labeling $48-61_amidated_fragment . mM 1.0 . stop_ save_ ############################ # Computer software used # ############################ save_NMRPIPE _Saveframe_category software _Name NMRPIPE _Version 5.0 _Details . _Citation_label $ref_1 save_ save_NMRView _Saveframe_category software _Name NMRView _Version 5.0 _Details . _Citation_label $ref_1 save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Inova _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H DQF-COSY' _Sample_label $sample_1 save_ save_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_1 save_ save_ROESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _Sample_label $sample_1 save_ save_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_Ex-cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 4.0 0.2 pH temperature 310 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 $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'amidated fragment 48-61' _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 LEU HA H 4.133 0.02 1 2 . 1 LEU HB2 H 1.793 0.02 2 3 . 1 LEU HB3 H 1.821 0.02 2 4 . 1 LEU HG H 1.001 0.02 1 5 . 2 SER H H 8.530 0.02 1 6 . 2 SER HA H 4.536 0.02 1 7 . 2 SER HB3 H 3.866 0.02 2 8 . 3 HIS H H 8.260 0.02 1 9 . 3 HIS HA H 4.758 0.02 1 10 . 3 HIS HB2 H 3.209 0.02 2 11 . 3 HIS HB3 H 3.281 0.02 2 12 . 3 HIS HE2 H 8.668 0.02 3 13 . 3 HIS HD1 H 7.736 0.02 3 14 . 4 GLY H H 8.317 0.02 1 15 . 4 GLY HA2 H 4.034 0.02 2 16 . 5 SER H H 8.150 0.02 1 17 . 5 SER HA H 4.479 0.02 1 18 . 5 SER HB3 H 3.906 0.02 2 19 . 6 ALA H H 8.119 0.02 1 20 . 6 ALA HA H 4.364 0.02 1 21 . 6 ALA HB H 1.413 0.02 1 22 . 7 GLN H H 8.073 0.02 1 23 . 7 GLN HA H 4.455 0.02 1 24 . 7 GLN HB2 H 2.008 0.02 2 25 . 7 GLN HB3 H 2.112 0.02 2 26 . 7 GLN HG3 H 2.359 0.02 2 27 . 7 GLN HE22 H 7.380 0.02 2 28 . 7 GLN HE21 H 6.693 0.02 2 29 . 8 VAL H H 7.942 0.02 1 30 . 8 VAL HA H 4.027 0.02 1 31 . 8 VAL HB H 2.147 0.02 1 32 . 8 VAL HG2 H 0.963 0.02 2 33 . 9 LYS H H 7.977 0.02 1 34 . 9 LYS HA H 4.241 0.02 1 35 . 9 LYS HB2 H 1.788 0.02 2 36 . 9 LYS HB3 H 1.873 0.02 2 37 . 9 LYS HG3 H 1.718 0.02 2 38 . 9 LYS HD2 H 1.486 0.02 2 39 . 9 LYS HE3 H 3.015 0.02 2 40 . 10 GLY H H 8.185 0.02 1 41 . 10 GLY HA2 H 3.906 0.02 2 42 . 11 HIS H H 8.168 0.02 1 43 . 11 HIS HA H 4.661 0.02 1 44 . 11 HIS HB2 H 3.253 0.02 2 45 . 11 HIS HB3 H 3.336 0.02 2 46 . 11 HIS HE2 H 8.694 0.02 3 47 . 11 HIS HD1 H 7.397 0.02 3 48 . 12 GLY H H 8.296 0.02 1 49 . 12 GLY HA2 H 4.000 0.02 2 50 . 13 ALA H H 8.110 0.02 1 51 . 13 ALA HA H 4.325 0.02 1 52 . 13 ALA HB H 1.418 0.02 1 53 . 14 LYS H H 8.009 0.02 1 54 . 14 LYS HA H 4.243 0.02 1 55 . 14 LYS HB2 H 1.818 0.02 2 56 . 14 LYS HB3 H 1.874 0.02 2 57 . 14 LYS HG3 H 1.705 0.02 2 58 . 14 LYS HD3 H 1.461 0.02 2 59 . 14 LYS HE3 H 3.015 0.02 2 60 . 14 LYS HZ H 7.409 0.02 1 61 . 15 NH2 HN1 H 6.900 0.02 2 62 . 15 NH2 HN2 H 7.290 0.02 2 stop_ save_