data_15272 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The NMR solution structure of a pH sensitive,D-amino acid containing conopeptide, mr12 . ; _BMRB_accession_number 15272 _BMRB_flat_file_name bmr15272.str _Entry_type original _Submission_date 2007-05-31 _Accession_date 2007-05-31 _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 Feijuan . . 2 Du Weihong . . 3 Han Yuhong . . 4 Wang Chunguang . . 5 Chi Chengwu . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 84 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-12 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 15273 'conopeptide mr12 mutant' stop_ _Original_release_date 2008-06-12 save_ ############################# # Citation for this entry # ############################# save_citation_1 _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 Yuhong . . 2 Huang Feijuan . . 3 Jiang Hui . . 4 Liu Li . . 5 Wang Qi . . 6 Wang Yanfang . . 7 Shao Xiaoxia . . 8 Chi Chengwu . . 9 Du Weihong . . 10 Wang Chunguang . . 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 . loop_ _Keyword 'M conotoxin' 'NMR solution structure' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'M cono-toxin mr12' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'chain A' $mr12_at_pH5 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_mr12_at_pH5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common mr12_at_pH5 _Molecular_mass 1935.080 _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 14 14:34:57 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 14:35:35 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 $mr12_at_pH5 'Conus marmoreus' 42752 Eukaryota Metazoa Conus marmoreus 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 $mr12_at_pH5 'chemical synthesis' . Conus marmoreus . . 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 $mr12_at_pH5 2.0 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $mr12_at_pH5 2.0 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 1.3 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.113 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9.0 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Koll' . . stop_ loop_ _Task refinement 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_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_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 5 . 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 $citation_1 $citation_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_chem-shift_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name '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 1 1 ASP HA H 4.274 0.004 . 2 1 1 ASP HB2 H 2.863 0.003 . 3 1 1 ASP HB3 H 2.782 0.001 . 4 2 2 TRP H H 8.753 0.002 . 5 2 2 TRP HA H 4.694 0.004 . 6 2 2 TRP HB2 H 3.290 0.002 2 7 2 2 TRP HD1 H 7.251 0.003 . 8 2 2 TRP HE1 H 10.170 0.002 . 9 2 2 TRP HE3 H 7.657 0.001 . 10 2 2 TRP HH2 H 7.290 0.003 . 11 2 2 TRP HZ2 H 7.538 0.003 . 12 2 2 TRP HZ3 H 7.183 0.001 . 13 3 3 GLU H H 8.159 0.002 . 14 3 3 GLU HA H 4.175 0.003 . 15 3 3 GLU HB2 H 1.757 0.002 . 16 3 3 GLU HB3 H 1.833 0.005 . 17 3 3 GLU HG2 H 2.103 0.003 2 18 4 4 TYR H H 8.153 0.002 . 19 4 4 TYR HA H 4.334 0.003 . 20 4 4 TYR HB2 H 2.866 0.003 . 21 4 4 TYR HB3 H 2.947 0.004 . 22 4 4 TYR HD1 H 7.104 0.003 3 23 4 4 TYR HE1 H 6.840 0.004 3 24 5 5 HIS H H 8.214 0.006 . 25 5 5 HIS HA H 4.545 0.004 . 26 5 5 HIS HB2 H 3.159 0.005 . 27 5 5 HIS HB3 H 3.019 0.005 . 28 5 5 HIS HD2 H 7.206 0.003 . 29 5 5 HIS HE1 H 8.566 0.003 . 30 6 6 ALA H H 8.312 0.003 . 31 6 6 ALA HA H 4.195 0.003 . 32 6 6 ALA HB H 1.368 0.003 . 33 7 7 HIS H H 8.560 0.001 . 34 7 7 HIS HA H 4.997 0.001 . 35 7 7 HIS HB2 H 3.265 0.003 . 36 7 7 HIS HB3 H 3.177 0.005 . 37 7 7 HIS HD2 H 7.371 0.001 . 38 7 7 HIS HE1 H 8.618 0.002 . 39 8 8 PRO HA H 4.457 0.004 . 40 8 8 PRO HB2 H 1.919 0.002 . 41 8 8 PRO HB3 H 2.272 0.004 . 42 8 8 PRO HD2 H 3.748 0.004 . 43 8 8 PRO HD3 H 3.580 0.004 . 44 8 8 PRO HG2 H 2.008 0.003 . 45 9 9 LYS H H 8.589 0.001 . 46 9 9 LYS HA H 4.580 0.000 . 47 9 9 LYS HB2 H 1.716 0.004 . 48 9 9 LYS HB3 H 1.812 0.004 . 49 9 9 LYS HD2 H 1.664 0.003 2 50 9 9 LYS HE2 H 2.968 0.000 2 51 9 9 LYS HG2 H 1.471 0.003 2 52 10 10 HYP HA H 4.585 0.006 . 53 10 10 HYP HB2 H 2.402 0.002 . 54 10 10 HYP HB3 H 2.396 0.002 . 55 10 10 HYP HD22 H 3.726 0.004 . 56 10 10 HYP HD23 H 3.890 0.004 . 57 10 10 HYP HG H 2.110 0.001 . 58 11 11 ASN H H 8.828 0.002 . 59 11 11 ASN HA H 4.593 0.004 . 60 11 11 ASN HB2 H 2.804 0.005 2 61 11 11 ASN HD21 H 6.981 0.001 . 62 11 11 ASN HD22 H 7.642 0.002 . 63 12 12 SER H H 8.156 0.002 . 64 12 12 SER HA H 4.333 0.004 . 65 12 12 SER HB2 H 3.698 0.002 . 66 12 12 SER HB3 H 3.757 0.004 . 67 13 13 DPN H H 8.047 0.003 . 68 13 13 DPN HA H 4.622 0.002 . 69 13 13 DPN HB2 H 2.832 0.005 . 70 13 13 DPN HB3 H 2.732 0.001 . 71 13 13 DPN HD1 H 7.298 0.005 3 72 13 13 DPN HE1 H 7.298 0.005 3 73 14 14 TRP H H 8.384 0.003 . 74 14 14 TRP HA H 4.864 0.001 . 75 14 14 TRP HB2 H 3.200 0.002 . 76 14 14 TRP HB3 H 3.426 0.005 . 77 14 14 TRP HD1 H 7.236 0.003 . 78 14 14 TRP HE1 H 10.175 0.006 . 79 14 14 TRP HE3 H 7.728 0.002 . 80 14 14 TRP HZ3 H 7.211 0.000 . 81 15 15 THR H H 7.867 0.004 . 82 15 15 THR HA H 4.291 0.003 . 83 15 15 THR HB H 4.248 0.000 . 84 15 15 THR HG2 H 1.192 0.005 . stop_ save_