data_4406 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The cyclic peptide contryphan-R from Conus radiatus ; _BMRB_accession_number 4406 _BMRB_flat_file_name bmr4406.str _Entry_type original _Submission_date 1999-09-15 _Accession_date 1999-09-16 _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 Pallaghy P. K. . 2 Melnikova A. P. . 3 Jimenez E. C. . 4 Olivera B. M. . 5 Norton R. S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 coupling_constants 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 49 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-17 update BMRB 'Updating non-standard residue' stop_ loop_ _Related_BMRB_accession_number _Relationship 4408 'minor form' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Pallaghy, P. K., Melnikova, A. P., Jimenez, E. C., Olivera, B. M., and Norton, R. S., "Solution structure of contryphan-R, a naturally occurring disulfide-bridged octapeptide containing D-tryptophan: comparison with protein loops," Biochemistry 38, 11553-11559 (1999). ; _Citation_title ; Solution structure of contryphan-R, a naturally occurring disulfide-bridged octapeptide containing D-tryptophan: comparison with protein loops ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99400497 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pallaghy P. K. . 2 Melnikova A. P. . 3 Jimenez E. C. . 4 Olivera B. M. . 5 Norton R. S. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 38 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11553 _Page_last 11559 _Year 1999 _Details . loop_ _Keyword 'cyclic peptide' 'disulfide bridge' D-configuration 'Conus peptide' 'stiff-tail syndrome' stop_ save_ ################################## # Molecular system description # ################################## save_system_contryphan-R _Saveframe_category molecular_system _Mol_system_name contryphan-R _Abbreviation_common contryphan-R _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'contryphan-R subunit 1' $contryphan-R stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'fully oxidized' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_contryphan-R _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common contryphan-R _Abbreviation_common contryphan-R _Molecular_mass . _Mol_thiol_state . _Details ; X3 = hydroxyproline = HYPR X4 = D-Tyrosine = DTR X8 = cysteinamide = CYS_NH2 ; ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence GCXXEPWCX loop_ _Residue_seq_code _Residue_label 1 GLY 2 CYS 3 HYP 4 DTR 5 GLU 6 PRO 7 TRP 8 CYS 9 NH2 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 Thu Jul 14 14:23:16 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_DTR _Saveframe_category polymer_residue _Mol_type 'D-peptide linking' _Name_common D-TRYPTOPHAN _BMRB_code . _PDB_code DTR _Standard_residue_derivative . _Molecular_mass 204.225 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jul 14 15:49:57 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 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? NE1 NE1 N . 0 . ? CE2 CE2 C . 0 . ? CZ2 CZ2 C . 0 . ? CH2 CH2 C . 0 . ? CZ3 CZ3 C . 0 . ? CE3 CE3 C . 0 . ? CD2 CD2 C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HZ2 HZ2 H . 0 . ? HH2 HH2 H . 0 . ? HZ3 HZ3 H . 0 . ? HE3 HE3 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 H ? ? SING N HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 NE1 ? ? SING CD1 HD1 ? ? SING NE1 CE2 ? ? SING NE1 HE1 ? ? DOUB CE2 CZ2 ? ? SING CE2 CD2 ? ? SING CZ2 CH2 ? ? SING CZ2 HZ2 ? ? DOUB CH2 CZ3 ? ? SING CH2 HH2 ? ? SING CZ3 CE3 ? ? SING CZ3 HZ3 ? ? DOUB CE3 CD2 ? ? SING CE3 HE3 ? ? 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 Thu Jul 14 10:32:06 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_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single disulfide 'contryphan-R subunit 1' 2 CYS SG 'contryphan-R subunit 1' 8 CYS SG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Tissue $contryphan-R 'Conus radiatus' 61998 Eukaryota Metazoa Conus radiatus 'venom duct' 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 $contryphan-R 'chemically synthesized' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'pH 3.0' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $contryphan-R 4.0 mM . stop_ save_ ############################ # Computer software used # ############################ save_XEASY _Saveframe_category software _Name XEASY _Version 1.3.13 loop_ _Task 'peak assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_1 save_ save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details '1D, NOESY, TCOSY, DQFCOSY' save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.0 0.2 n/a temperature 278 0.5 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_chem_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'contryphan-R subunit 1' _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 3.88 . 1 2 . 1 GLY HA3 H 3.88 . 1 3 . 2 CYS H H 8.51 . 1 4 . 2 CYS HA H 4.73 . 1 5 . 2 CYS HB2 H 2.57 . 1 6 . 2 CYS HB3 H 3.04 . 1 7 . 3 HYP HA H 4.49 . 1 8 . 3 HYP HB2 H 1.21 . 1 9 . 3 HYP HB3 H 2.12 . 1 10 . 3 HYP HG H 2.12 . 1 11 . 3 HYP HD22 H 3.88 . 1 12 . 3 HYP HD23 H 3.88 . 1 13 . 4 DTR H H 8.85 . 1 14 . 4 DTR HA H 5.05 . 1 15 . 4 DTR HB2 H 3.06 . 1 16 . 4 DTR HB3 H 3.32 . 1 17 . 4 DTR HD1 H 7.18 . 1 18 . 4 DTR HE1 H 10.15 . 1 19 . 4 DTR HE3 H 7.50 . 1 20 . 4 DTR HZ2 H 7.44 . 1 21 . 4 DTR HZ3 H 7.04 . 1 22 . 4 DTR HH2 H 7.17 . 1 23 . 5 GLU H H 6.90 . 1 24 . 5 GLU HA H 4.67 . 1 25 . 5 GLU HB2 H 0.25 . 1 26 . 5 GLU HB3 H 0.62 . 1 27 . 5 GLU HG2 H 2.19 . 1 28 . 5 GLU HG3 H 2.31 . 1 29 . 6 PRO HA H 4.10 . 1 30 . 6 PRO HB2 H 2.08 . 1 31 . 6 PRO HB3 H 2.39 . 1 32 . 6 PRO HG2 H 2.10 . 1 33 . 6 PRO HG3 H 2.16 . 1 34 . 6 PRO HD2 H 3.41 . 1 35 . 6 PRO HD3 H 3.62 . 1 36 . 7 TRP H H 6.29 . 1 37 . 7 TRP HA H 4.75 . 1 38 . 7 TRP HB2 H 3.25 . 1 39 . 7 TRP HB3 H 3.56 . 1 40 . 7 TRP HD1 H 7.10 . 1 41 . 7 TRP HE1 H 10.35 . 1 42 . 7 TRP HE3 H 7.61 . 1 43 . 7 TRP HZ2 H 7.42 . 1 44 . 7 TRP HZ3 H 7.20 . 1 45 . 7 TRP HH2 H 7.17 . 1 46 . 8 CYS H H 7.10 . 1 47 . 8 CYS HA H 4.26 . 1 48 . 8 CYS HB2 H 3.05 . 1 49 . 8 CYS HB3 H 3.11 . 1 stop_ save_