data_16785 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; solution structure of cis-4-hydroxyproline contained conotoxin cis-mr3c ; _BMRB_accession_number 16785 _BMRB_flat_file_name bmr16785.str _Entry_type new _Submission_date 2010-03-22 _Accession_date 2010-03-22 _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 Xu Jia . . 2 Du Weihong . . 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 2010-07-27 update BMRB 'Complete entry citation' 2010-06-03 update BMRB 'edit assembly name' 2010-05-03 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16784 conotoxin_mr3c 16786 cis-conomarphin stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Stereochemistry of 4-hydroxyproline affects the conformation of conopeptides.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20428585 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Xu Jia . . 2 Wang Yanli . . 3 Zhang Bingbing . . 4 Wang Baohuai . . 5 Du Weihong . . stop_ _Journal_abbreviation 'Chem. Commun. (Camb.)' _Journal_name_full 'Chemical communications (Cambridge, England)' _Journal_volume 46 _Journal_issue 30 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5467 _Page_last 5469 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'conotoxin cis-mr3c' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label conotoxin_cis-mr3c $conotoxin_cis-mr3c 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_conotoxin_cis-mr3c _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common conotoxin_cis-mr3c _Molecular_mass 1604.994 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence CCAPSACRLGCRXCCR loop_ _Residue_seq_code _Residue_label 1 CYS 2 CYS 3 ALA 4 PRO 5 SER 6 ALA 7 CYS 8 ARG 9 LEU 10 GLY 11 CYS 12 ARG 13 GPR 14 CYS 15 CYS 16 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_GPR _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE _BMRB_code . _PDB_code GPR _Standard_residue_derivative . _Molecular_mass 501.552 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 14:22:24 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 0 . ? CA1 CA1 C . 0 . ? C1 C1 C . 0 . ? O11 O11 O . 0 . ? O12 O12 O . 0 . ? CB1 CB1 C . 0 . ? CG1 CG1 C . 0 . ? CD1 CD1 C . 0 . ? OE1 OE1 O . 0 . ? N2 N2 N . 0 . ? CA2 CA2 C . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? CB2 CB2 C . 0 . ? SG2 SG2 S . 0 . ? N3 N3 N . 0 . ? CA3 CA3 C . 0 . ? C3 C3 C . 0 . ? O31 O31 O . 0 . ? O32 O32 O . 0 . ? CA4 CA4 C . 0 . ? CB4 CB4 C . 0 . ? CG4 CG4 C . 0 . ? CD4 CD4 C . 0 . ? CE4 CE4 C . 0 . ? CZ4 CZ4 C . 0 . ? CH4 CH4 C . 0 . ? CH5 CH5 C . 0 . ? CZ5 CZ5 C . 0 . ? CE5 CE5 C . 0 . ? CD5 CD5 C . 0 . ? CG5 CG5 C . 0 . ? CB5 CB5 C . 0 . ? CA5 CA5 C . 0 . ? O5 O5 O . 0 . ? HN11 HN11 H . 0 . ? HN12 HN12 H . 0 . ? HA1 HA1 H . 0 . ? HO2 HO2 H . 0 . ? HB11 HB11 H . 0 . ? HB12 HB12 H . 0 . ? HG11 HG11 H . 0 . ? HG12 HG12 H . 0 . ? HN2 HN2 H . 0 . ? HA2 HA2 H . 0 . ? HB21 HB21 H . 0 . ? HB22 HB22 H . 0 . ? HN3 HN3 H . 0 . ? HA31 HA31 H . 0 . ? HA32 HA32 H . 0 . ? HO3 HO3 H . 0 . ? HA4 HA4 H . 0 . ? HG4 HG4 H . 0 . ? HD4 HD4 H . 0 . ? HE4 HE4 H . 0 . ? HZ4 HZ4 H . 0 . ? HZ5 HZ5 H . 0 . ? HE5 HE5 H . 0 . ? HD5 HD5 H . 0 . ? HG5 HG5 H . 0 . ? HA5 HA5 H . 0 . ? HO5 HO5 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 N1 CA1 ? ? SING N1 HN11 ? ? SING N1 HN12 ? ? SING CA1 C1 ? ? SING CA1 CB1 ? ? SING CA1 HA1 ? ? DOUB C1 O11 ? ? SING C1 O12 ? ? SING O12 HO2 ? ? SING CB1 CG1 ? ? SING CB1 HB11 ? ? SING CB1 HB12 ? ? SING CG1 CD1 ? ? SING CG1 HG11 ? ? SING CG1 HG12 ? ? DOUB CD1 OE1 ? ? SING CD1 N2 ? ? SING N2 CA2 ? ? SING N2 HN2 ? ? SING CA2 C2 ? ? SING CA2 CB2 ? ? SING CA2 HA2 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING CB2 SG2 ? ? SING CB2 HB21 ? ? SING CB2 HB22 ? ? SING SG2 CA4 ? ? SING N3 CA3 ? ? SING N3 HN3 ? ? SING CA3 C3 ? ? SING CA3 HA31 ? ? SING CA3 HA32 ? ? DOUB C3 O31 ? ? SING C3 O32 ? ? SING O32 HO3 ? ? SING CA4 CB4 ? ? SING CA4 CA5 ? ? SING CA4 HA4 ? ? DOUB CB4 CG4 ? ? SING CB4 CH4 ? ? SING CG4 CD4 ? ? SING CG4 HG4 ? ? DOUB CD4 CE4 ? ? SING CD4 HD4 ? ? SING CE4 CZ4 ? ? SING CE4 HE4 ? ? DOUB CZ4 CH4 ? ? SING CZ4 HZ4 ? ? SING CH4 CH5 ? ? SING CH5 CZ5 ? ? DOUB CH5 CB5 ? ? DOUB CZ5 CE5 ? ? SING CZ5 HZ5 ? ? SING CE5 CD5 ? ? SING CE5 HE5 ? ? DOUB CD5 CG5 ? ? SING CD5 HD5 ? ? SING CG5 CB5 ? ? SING CG5 HG5 ? ? SING CB5 CA5 ? ? SING CA5 O5 ? ? SING CA5 HA5 ? ? SING O5 HO5 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $conotoxin_cis-mr3c gastropods 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 $conotoxin_cis-mr3c 'chemical synthesis' . . . . . 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 $conotoxin_cis-mr3c 4 mM 'natural abundance' TFA 0.01 % 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $conotoxin_cis-mr3c 4 mM 'natural abundance' TFA 0.01 % 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing 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 'structure solution' 'geometry optimization' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 10.0 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' 'chemical shift assignment' 'data analysis' 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_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _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 pH 3.0 . pH pressure 1 . atm temperature 283 . 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 protons' ppm 0.00 internal direct . . . 1.000000000 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 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 conotoxin_cis-mr3c _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 CYS HA H 4.370 0.002 1 2 1 1 CYS HB2 H 3.068 0.003 2 3 1 1 CYS HB3 H 2.899 0.003 2 4 2 2 CYS H H 9.455 0.002 1 5 2 2 CYS HA H 4.764 0.002 1 6 2 2 CYS HB2 H 3.334 0.004 2 7 2 2 CYS HB3 H 2.789 0.001 2 8 3 3 ALA H H 9.414 0.003 1 9 3 3 ALA HA H 4.506 0.004 1 10 3 3 ALA HB H 1.575 0.002 . 11 4 4 PRO HA H 4.257 0.003 1 12 4 4 PRO HB2 H 2.400 0.003 2 13 4 4 PRO HB3 H 2.003 0.004 2 14 4 4 PRO HD2 H 3.889 0.004 2 15 4 4 PRO HD3 H 3.802 0.003 2 16 4 4 PRO HG2 H 2.221 0.003 2 17 4 4 PRO HG3 H 2.221 0.003 2 18 5 5 SER H H 8.838 0.003 1 19 5 5 SER HA H 4.079 0.001 1 20 5 5 SER HB2 H 3.901 0.004 2 21 5 5 SER HB3 H 3.901 0.004 2 22 6 6 ALA H H 7.178 0.003 1 23 6 6 ALA HA H 4.353 0.002 1 24 6 6 ALA HB H 1.553 0.003 . 25 7 7 CYS H H 9.142 0.003 1 26 7 7 CYS HA H 4.745 0.004 1 27 7 7 CYS HB2 H 3.547 0.001 2 28 7 7 CYS HB3 H 2.959 0.004 2 29 8 8 ARG H H 8.056 0.001 1 30 8 8 ARG HA H 4.161 0.002 1 31 8 8 ARG HB2 H 1.957 0.002 2 32 8 8 ARG HB3 H 1.751 0.001 2 33 8 8 ARG HD2 H 3.226 0.001 2 34 8 8 ARG HD3 H 3.226 0.001 2 35 8 8 ARG HG2 H 1.671 0.004 2 36 8 8 ARG HG3 H 1.671 0.004 2 37 8 8 ARG HH21 H 6.975 0.001 2 38 8 8 ARG HH22 H 6.682 0.000 2 39 9 9 LEU H H 7.251 0.005 1 40 9 9 LEU HA H 4.458 0.003 1 41 9 9 LEU HB2 H 1.860 0.002 2 42 9 9 LEU HB3 H 1.775 0.001 2 43 9 9 LEU HD1 H 0.932 0.003 . 44 9 9 LEU HD2 H 0.884 0.002 . 45 10 10 GLY H H 7.748 0.002 1 46 10 10 GLY HA2 H 4.493 0.004 2 47 10 10 GLY HA3 H 3.603 0.002 2 48 11 11 CYS H H 7.648 0.002 1 49 11 11 CYS HA H 4.415 0.002 1 50 11 11 CYS HB2 H 2.888 0.005 2 51 11 11 CYS HB3 H 2.569 0.004 2 52 12 12 ARG H H 8.786 0.003 1 53 12 12 ARG HA H 4.625 0.003 1 54 12 12 ARG HD2 H 3.572 0.002 2 55 12 12 ARG HD3 H 3.166 0.003 2 56 12 12 ARG HG2 H 1.691 0.002 2 57 12 12 ARG HG3 H 1.691 0.002 2 58 12 12 ARG HH21 H 6.973 0.003 2 59 12 12 ARG HH22 H 6.685 0.005 2 60 13 13 GPR HA H 4.546 0.004 . 61 13 13 GPR HB2 H 2.697 0.004 . 62 13 13 GPR HB3 H 2.079 0.005 . 63 13 13 GPR HD2 H 3.882 0.004 . 64 13 13 GPR HD3 H 3.499 0.004 . 65 14 14 CYS H H 9.671 0.002 1 66 14 14 CYS HA H 4.854 0.004 1 67 14 14 CYS HB2 H 3.591 0.005 2 68 14 14 CYS HB3 H 3.254 0.003 2 69 15 15 CYS H H 9.024 0.003 1 70 15 15 CYS HA H 4.548 0.003 1 71 15 15 CYS HB2 H 3.367 0.004 2 72 15 15 CYS HB3 H 2.631 0.003 2 73 16 16 ARG H H 8.595 0.003 1 74 16 16 ARG HA H 4.263 0.003 1 75 16 16 ARG HB2 H 1.913 0.001 2 76 16 16 ARG HB3 H 1.748 0.003 2 77 16 16 ARG HD2 H 1.639 0.002 2 78 16 16 ARG HD3 H 1.639 0.002 2 stop_ save_