data_7397 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Purification and structural characterization of a D-amino acid containing conopeptide, marmophine, from Conus marmoreus ; _BMRB_accession_number 7397 _BMRB_flat_file_name bmr7397.str _Entry_type original _Submission_date 2007-06-29 _Accession_date 2007-08-30 _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 Huang F. J. . 2 Du W. H. . 3 Han Y. H. . 4 Wang C. G. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 78 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-17 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Purification and structural characterization of a D-amino acid-containing conopeptide, conomarphin, from Conus marmoreus' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18355315 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Han Y. H. . 2 Huang F. J. . 3 Jiang H. . . 4 Liu L. . . 5 Wang Q. . . 6 Wang Y. H. . 7 Shao X. G. . 8 Chi C. . . 9 Du W. . . 10 Wang C. . . stop_ _Journal_abbreviation 'FEBS J.' _Journal_volume 275 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1976 _Page_last 1987 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name M-conotoxin_mr12 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label M-conotoxin_mr12 $M-conotoxin_mr12 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details ; _struct_conn.id _struct_conn.conn_type_id _struct_conn.ndb_PDB_id _struct_conn.ndb_ptnr1_mod_name _struct_conn.ndb_ptnr1_replaced_atom _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ndb_ptnr1_label_alt_loc _struct_conn.ndb_ptnr1_label_ins_code _struct_conn.ndb_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ndb_ptnr2_label_alt_loc _struct_conn.ndb_ptnr2_label_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.ndb_ptnr3_label_atom_id _struct_conn.ndb_ptnr3_label_seq_id _struct_conn.ndb_ptnr3_label_comp_id _struct_conn.ndb_ptnr3_label_asym_id _struct_conn.ndb_ptnr3_label_alt_loc _struct_conn.ndb_ptnr3_label_ins_code _struct_conn.details modres1 modres 2YYF ? ? A HYP 10 ? ? ? PRO 1_555 ? ? ? ? ? ? A HYP 10 ? ? ? 1_555 ? ? ? ? ? ? 4-HYDROXYPROLINE modres2 modres 2YYF ? ? A DPN 13 ? ? ? PHE 1_555 ? ? ? ? ? ? A DPN 13 ? ? ? 1_555 ? ? ? ? ? ? D-PHENYLALANINE # ; save_ ######################## # Monomeric polymers # ######################## save_M-conotoxin_mr12 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common M-conotoxin_mr12 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence DWEYHAHPKXNSXWT loop_ _Residue_seq_code _Residue_label 1 ASP 2 TRP 3 GLU 4 TYR 5 HIS 6 ALA 7 HIS 8 PRO 9 LYS 10 HYP 11 ASN 12 SER 13 DPN 14 TRP 15 THR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_HYP _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 4-HYDROXYPROLINE _BMRB_code . _PDB_code HYP _Standard_residue_derivative . _Molecular_mass 131.130 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Oct 7 14:10:58 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 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OD1 OD1 O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG H . 0 . ? HD22 HD22 H . 0 . ? HD23 HD23 H . 0 . ? HD1 HD1 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG OD1 ? ? SING CG HG ? ? SING CD HD22 ? ? SING CD HD23 ? ? SING OD1 HD1 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DPN _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-PHENYLALANINE _BMRB_code . _PDB_code DPN _Standard_residue_derivative . _Molecular_mass 165.189 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Oct 14 14:41:04 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 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? CZ CZ C . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? HZ HZ 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 H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 CE1 ? ? SING CD1 HD1 ? ? DOUB CD2 CE2 ? ? SING CD2 HD2 ? ? DOUB CE1 CZ ? ? SING CE1 HE1 ? ? SING CE2 CZ ? ? SING CE2 HE2 ? ? SING CZ HZ ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $M-conotoxin_mr12 'Shigella flexneri' 623 Bacteria . Shigella flexneri 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 $M-conotoxin_mr12 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2.0mM, 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $M-conotoxin_mr12 2.0 mM 'natural abundance' H2O 90 % . D2O 10 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '2.0mM, 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $M-conotoxin_mr12 2.0 mM 'natural abundance' D2O 99.99 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker Inc.' . . stop_ loop_ _Task collection stop_ _Details . save_ save_Topspin _Saveframe_category software _Name Topspin _Version 1.3B loop_ _Vendor _Address _Electronic_address 'Bruker Inc.' . . stop_ loop_ _Task processing stop_ _Details . save_ save_Sparky _Saveframe_category software _Name Sparky _Version 3.110 loop_ _Vendor _Address _Electronic_address 'T. D. Goddard and D. G. Kneller' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'L. A. Systems, Inc.' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9.0 loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_2D_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_DQF-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.0 . pH pressure 1 . atm temperature 300 . K 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 carbons' ppm 0 external 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 NOESY' '2D TOCSY' DQF-COSY stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name M-conotoxin_mr12 _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 ASP HA H 4.193 0.001 . 2 1 1 ASP HB2 H 2.816 0.002 . 3 2 2 TRP H H 8.558 0.002 . 4 2 2 TRP HA H 4.565 0.001 . 5 2 2 TRP HB2 H 3.140 0.002 2 6 2 2 TRP HD1 H 7.117 0.001 . 7 2 2 TRP HE1 H 9.987 0.003 . 8 2 2 TRP HE3 H 7.496 0.004 . 9 2 2 TRP HH2 H 7.136 0.004 . 10 2 2 TRP HZ2 H 7.385 0.004 . 11 2 2 TRP HZ3 H 7.037 0.004 . 12 3 3 GLU H H 7.849 0.004 . 13 3 3 GLU HA H 4.037 0.002 . 14 3 3 GLU HB2 H 1.693 0.002 . 15 3 3 GLU HB3 H 1.581 0.002 . 16 3 3 GLU HG2 H 2.010 0.004 2 17 4 4 TYR H H 7.869 0.004 . 18 4 4 TYR HA H 4.180 0.003 . 19 4 4 TYR HB2 H 2.772 0.002 . 20 4 4 TYR HB3 H 2.725 0.001 . 21 4 4 TYR HD1 H 6.951 0.002 3 22 4 4 TYR HE1 H 6.688 0.002 3 23 5 5 HIS H H 8.028 0.003 . 24 5 5 HIS HA H 4.407 0.002 . 25 5 5 HIS HB2 H 3.024 2.882 . 26 5 5 HIS HB3 H 2.882 0.002 . 27 5 5 HIS HD2 H 7. 0.002 . 28 6 6 ALA H H 8.087 0.003 . 29 6 6 ALA HA H 4.058 0.001 . 30 6 6 ALA HB H 1.219 0.003 . 31 7 7 HIS H H 8.389 0.002 . 32 7 7 HIS HA H 4.841 0.003 . 33 7 7 HIS HB2 H 3.034 0.004 . 34 7 7 HIS HB3 H 3.122 0.004 . 35 7 7 HIS HD2 H 7.231 0.002 . 36 8 8 PRO HA H 4.318 0.005 . 37 8 8 PRO HB2 H 2.131 0.003 2 38 8 8 PRO HD2 H 3.601 0.002 . 39 8 8 PRO HD3 H 3.411 0.003 . 40 8 8 PRO HG2 H 1.775 0.005 . 41 8 8 PRO HG3 H 1.854 0.004 . 42 9 9 LYS H H 8.382 0.001 . 43 9 9 LYS HA H 4.449 0.002 . 44 9 9 LYS HB2 H 1.677 0.004 . 45 9 9 LYS HB3 H 1.587 0.003 . 46 9 9 LYS HD2 H 1.530 0.008 2 47 9 9 LYS HE2 H 2.843 0.004 2 48 9 9 LYS HG2 H 1.346 0.005 2 49 10 10 HYP HA H 4.440 0.000 . 50 10 10 HYP HB2 H 2.249 0.002 2 51 10 10 HYP HD22 H 3.752 0.002 . 52 10 10 HYP HD23 H 3.621 0.001 . 53 10 10 HYP HG H 1.957 0.003 . 54 11 11 ASN H H 8.606 0.001 . 55 11 11 ASN HA H 4.460 0.005 . 56 11 11 ASN HB2 H 2.657 0.002 2 57 12 12 SER H H 7.967 0.003 . 58 12 12 SER HA H 4.213 0.001 . 59 12 12 SER HB2 H 3.596 0.009 . 60 12 12 SER HB3 H 3.568 0.005 . 61 13 13 DPN H H 7.932 0.006 . 62 13 13 DPN HA H 4.485 0.003 . 63 13 13 DPN HB2 H 2.749 0.005 . 64 13 13 DPN HB3 H 2.659 0.001 . 65 13 13 DPN HD1 H 6.926 0.003 3 66 13 13 DPN HE1 H 7.163 0.001 3 67 14 14 TRP H H 8.148 0.003 . 68 14 14 TRP HA H 4.663 0.003 . 69 14 14 TRP HB2 H 3.209 0.003 . 70 14 14 TRP HB3 H 3.030 0.002 . 71 14 14 TRP HD1 H 7.072 0.003 . 72 14 14 TRP HE1 H 9.985 0.004 . 73 14 14 TRP HE3 H 7.537 0.003 . 74 14 14 TRP HZ3 H 7.069 0.005 . 75 15 15 THR H H 7.876 0.002 . 76 15 15 THR HA H 4.265 0.002 . 77 15 15 THR HB H 4.200 0.002 . 78 15 15 THR HG2 H 1.042 0.002 . stop_ save_