data_4194 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural Studies of D-Pro Melittin ; _BMRB_accession_number 4194 _BMRB_flat_file_name bmr4194.str _Entry_type original _Submission_date 1998-09-04 _Accession_date 1998-09-04 _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 Hewish D. . . 2 Werkmeister J. . . 3 Curtain C. . . 4 Kirkpatrick A. . . 5 Bartone N. . . 6 Barnham K. J. . 7 Ting S. . . 8 Norton R. . . 9 Rivett D. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 126 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-05-21 update BMRB 'modified residue was added' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure-Functional Activity Studies of D-Pro Melittin' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12168695 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hewish D. R. . 2 Barnham K. J. . 3 Werkmeister J. A. . 4 Kirkpatrick A. . . 5 Bartone N. . . 6 Liu S. T. . 7 Norton R. S. . 8 Curtain C. . . 9 Rivett D. . . stop_ _Journal_abbreviation 'J. Protein Chem.' _Journal_volume 21 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 243 _Page_last 253 _Year 2002 _Details . loop_ _Keyword 'hemolytic polypeptide' toxin stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_one _Saveframe_category citation _Citation_full ; Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J., Oldfield, E., Markley, J. L., and Sykes, B. D. J. Biomol. NMR 6, 135-140 (1995). ; _Citation_title '1H, 13C and 15N chemical shift referencing in biomolecular NMR.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8589602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wishart 'D S' S. . 2 Bigam 'C G' G. . 3 Yao J . . 4 Abildgaard F . . 5 Dyson 'H J' J. . 6 Oldfield E . . 7 Markley 'J L' L. . 8 Sykes 'B D' D. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 2 _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 135 _Page_last 140 _Year 1995 _Details ; A considerable degree of variability exists in the way that 1H, 13C and 15N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common 1H, 13C and 15N chemical shift standards, now used in biomolecular NMR, to those proposed here. ; save_ ################################## # Molecular system description # ################################## save_system_D-Pro_melittin _Saveframe_category molecular_system _Mol_system_name 'D-Pro melittin' _Abbreviation_common 'D-Pro melittin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'D-Pro melittin' $D-Pro_melittin 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_D-Pro_melittin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'D-Pro melittin' _Name_variant 'P 14 D-Pro' _Abbreviation_common 'D-Pro melittin' _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; GIGAVLKVLTTGLXALISWI KRKRQQX ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 GLY 4 ALA 5 VAL 6 LEU 7 LYS 8 VAL 9 LEU 10 THR 11 THR 12 GLY 13 LEU 14 DPR 15 ALA 16 LEU 17 ILE 18 SER 19 TRP 20 ILE 21 LYS 22 ARG 23 LYS 24 ARG 25 GLN 26 GLN 27 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2005-12-09 save_ ###################### # Polymer residues # ###################### save_chem_comp_DPR _Saveframe_category polymer_residue _Mol_type 'D-Peptide Linking' _Name_common D-PROLINE _BMRB_code . _PDB_code DPR _Standard_residue_derivative . _Molecular_mass 115.130 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Aug 25 09:36:06 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 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 SING N CA ? ? SING N CD ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD HD2 ? ? SING CD HD3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ 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 Wed Jun 22 17:31:31 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 $D-Pro_melittin . . . . . . 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 $D-Pro_melittin 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $D-Pro_melittin . mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_one save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_one save_ save_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _Sample_label $sample_one save_ save_E-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label $sample_one save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 2 . mM pH 5.2 0.2 pH pressure 1 . atm temperature 277 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 _Indirect_shift_ratio_citation_label DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.0 $citation_one 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_chemical_shifts_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name 'D-Pro melittin' _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 GLY HA2 H 3.91 . 1 2 . 1 GLY HA3 H 3.91 . 1 3 . 2 ILE H H 9.15 . 1 4 . 2 ILE HA H 4.07 . 1 5 . 2 ILE HB H 1.93 . 1 6 . 2 ILE HG12 H 1.07 . 1 7 . 2 ILE HG13 H 1.07 . 1 8 . 3 GLY H H 9.05 . 1 9 . 3 GLY HA2 H 3.80 . 2 10 . 3 GLY HA3 H 3.90 . 2 11 . 4 ALA H H 8.01 . 1 12 . 4 ALA HA H 4.12 . 1 13 . 4 ALA HB H 1.58 . 1 14 . 5 VAL H H 7.58 . 1 15 . 5 VAL HA H 3.61 . 1 16 . 5 VAL HB H 2.35 . 1 17 . 5 VAL HG1 H 1.14 . 2 18 . 5 VAL HG2 H 1.35 . 1 19 . 12 GLY H H 8.26 . 1 20 . 12 GLY HA2 H 4.14 . 2 21 . 12 GLY HA3 H 4.02 . 2 22 . 13 LEU H H 8.37 . 1 23 . 13 LEU HA H 4.54 . 1 24 . 13 LEU HB2 H 1.81 . 1 25 . 13 LEU HB3 H 1.81 . 1 26 . 13 LEU HG H 1.58 . 1 27 . 13 LEU HD1 H 1.02 . 1 28 . 13 LEU HD2 H 1.02 . 1 29 . 14 DPR HA H 4.41 . 1 30 . 14 DPR HB2 H 2.31 . 2 31 . 14 DPR HB3 H 2.09 . 2 32 . 14 DPR HG2 H 2.17 . 2 33 . 14 DPR HG3 H 2.17 . 2 34 . 14 DPR HD2 H 3.73 . 2 35 . 14 DPR HD3 H 3.98 . 2 36 . 15 ALA H H 8.40 . 1 37 . 15 ALA HA H 4.25 . 1 38 . 15 ALA HB H 1.54 . 1 39 . 16 LEU H H 8.34 . 1 40 . 16 LEU HA H 4.28 . 1 41 . 16 LEU HB2 H 1.95 . 1 42 . 16 LEU HB3 H 1.95 . 1 43 . 16 LEU HG H 1.77 . 1 44 . 16 LEU HD1 H 1.00 . 2 45 . 16 LEU HD2 H 1.08 . 2 46 . 17 ILE H H 8.10 . 1 47 . 17 ILE HA H 3.97 . 1 48 . 17 ILE HB H 2.00 . 1 49 . 17 ILE HG2 H 1.33 . 1 50 . 17 ILE HG12 H 1.67 . 1 51 . 17 ILE HG13 H 1.67 . 1 52 . 17 ILE HD1 H 1.02 . 1 53 . 18 SER H H 7.69 . 1 54 . 18 SER HA H 4.19 . 1 55 . 18 SER HB2 H 4.06 . 2 56 . 18 SER HB3 H 3.94 . 2 57 . 19 TRP H H 8.33 . 1 58 . 19 TRP HA H 4.36 . 1 59 . 19 TRP HB2 H 3.50 . 2 60 . 19 TRP HB3 H 3.41 . 2 61 . 19 TRP HD1 H 7.23 . 1 62 . 19 TRP HE3 H 7.59 . 1 63 . 19 TRP HE1 H 10.51 . 1 64 . 19 TRP HZ3 H 7.04 . 1 65 . 19 TRP HZ2 H 7.43 . 1 66 . 19 TRP HH2 H 7.14 . 1 67 . 20 ILE H H 8.44 . 1 68 . 20 ILE HA H 3.62 . 1 69 . 20 ILE HB H 2.06 . 1 70 . 20 ILE HG2 H 0.99 . 1 71 . 20 ILE HG12 H 1.23 . 1 72 . 20 ILE HG13 H 1.23 . 1 73 . 21 LYS H H 8.28 . 1 74 . 21 LYS HA H 3.94 . 1 75 . 21 LYS HB2 H 2.03 . 1 76 . 21 LYS HB3 H 2.03 . 1 77 . 21 LYS HG2 H 1.46 . 1 78 . 21 LYS HG3 H 1.46 . 1 79 . 21 LYS HD2 H 1.73 . 1 80 . 21 LYS HD3 H 1.73 . 1 81 . 21 LYS HE2 H 3.15 . 2 82 . 21 LYS HE3 H 3.23 . 2 83 . 21 LYS HZ H 7.59 . 1 84 . 22 ARG H H 8.25 . 1 85 . 22 ARG HA H 4.12 . 1 86 . 22 ARG HB2 H 1.95 . 2 87 . 22 ARG HB3 H 1.77 . 2 88 . 22 ARG HG2 H 1.68 . 1 89 . 22 ARG HG3 H 1.68 . 1 90 . 22 ARG HD2 H 2.83 . 1 91 . 22 ARG HD3 H 2.83 . 1 92 . 23 LYS H H 8.37 . 1 93 . 23 LYS HA H 4.05 . 1 94 . 23 LYS HB2 H 1.81 . 2 95 . 23 LYS HB3 H 1.95 . 2 96 . 23 LYS HG2 H 1.33 . 1 97 . 23 LYS HG3 H 1.33 . 1 98 . 23 LYS HD2 H 1.55 . 1 99 . 23 LYS HD3 H 1.55 . 1 100 . 23 LYS HE2 H 2.94 . 1 101 . 23 LYS HE3 H 2.94 . 1 102 . 24 ARG H H 8.29 . 1 103 . 24 ARG HA H 4.11 . 1 104 . 24 ARG HB2 H 1.94 . 2 105 . 24 ARG HB3 H 2.02 . 2 106 . 24 ARG HG2 H 1.71 . 1 107 . 24 ARG HG3 H 1.71 . 1 108 . 24 ARG HD2 H 3.16 . 1 109 . 24 ARG HD3 H 3.16 . 1 110 . 24 ARG HE H 7.45 . 1 111 . 25 GLN H H 8.05 . 1 112 . 25 GLN HA H 4.14 . 1 113 . 25 GLN HB2 H 2.34 . 2 114 . 25 GLN HB3 H 2.17 . 2 115 . 25 GLN HG2 H 2.65 . 2 116 . 25 GLN HG3 H 2.38 . 2 117 . 25 GLN HE21 H 7.69 . 2 118 . 25 GLN HE22 H 6.95 . 2 119 . 26 GLN H H 7.86 . 1 120 . 26 GLN HA H 4.21 . 1 121 . 26 GLN HB2 H 2.20 . 2 122 . 26 GLN HB3 H 2.36 . 2 123 . 26 GLN HG2 H 2.63 . 1 124 . 26 GLN HG3 H 2.63 . 1 125 . 26 GLN HE21 H 7.71 . 2 126 . 26 GLN HE22 H 6.99 . 2 stop_ save_