data_16786 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; solution structure of 4-hydroxyproline contained cis-conomarphin ; _BMRB_accession_number 16786 _BMRB_flat_file_name bmr16786.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" 85 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-28 update BMRB 'update 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 16785 conotoxin_cis-mr3c 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 cis-conomarphin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label cis-conomarphin $cis-conomarphin 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_cis-conomarphin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cis-conomarphin _Molecular_mass 1914.90 _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 GPR 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_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 Tue Jun 9 13:50:48 2009 ; 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_ 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 $cis-conomarphin 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 $cis-conomarphin '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 $cis-conomarphin 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 $cis-conomarphin 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 cis-conomarphin _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 4.290 0.004 1 2 1 1 ASP HB2 H 2.920 0.000 2 3 1 1 ASP HB3 H 2.920 0.000 2 4 2 2 TRP H H 8.706 0.002 1 5 2 2 TRP HA H 4.644 0.004 1 6 2 2 TRP HB2 H 3.231 0.002 2 7 2 2 TRP HB3 H 3.231 0.002 2 8 2 2 TRP HD1 H 7.207 0.002 1 9 2 2 TRP HE1 H 10.108 0.002 1 10 2 2 TRP HE3 H 7.579 0.002 1 11 2 2 TRP HH2 H 7.215 0.002 1 12 2 2 TRP HZ2 H 7.469 0.003 1 13 2 2 TRP HZ3 H 7.112 0.000 1 14 3 3 GLU H H 7.961 0.003 1 15 3 3 GLU HA H 4.114 0.005 1 16 3 3 GLU HB2 H 1.765 0.004 2 17 3 3 GLU HB3 H 1.659 0.005 2 18 3 3 GLU HG2 H 2.081 0.005 2 19 3 3 GLU HG3 H 2.081 0.005 2 20 4 4 TYR H H 8.019 0.003 1 21 4 4 TYR HA H 4.248 0.004 1 22 4 4 TYR HB2 H 2.876 0.004 2 23 4 4 TYR HB3 H 2.798 0.004 2 24 4 4 TYR HD1 H 7.039 0.002 3 25 4 4 TYR HD2 H 7.039 0.002 3 26 4 4 TYR HE1 H 6.773 0.003 3 27 4 4 TYR HE2 H 6.773 0.003 3 28 5 5 HIS H H 8.137 0.003 1 29 5 5 HIS HA H 4.477 0.005 1 30 5 5 HIS HB2 H 3.092 0.004 2 31 5 5 HIS HB3 H 2.951 0.002 2 32 5 5 HIS HD2 H 7.144 0.003 1 33 6 6 ALA H H 8.236 0.001 1 34 6 6 ALA HA H 4.124 0.002 1 35 6 6 ALA HB H 1.305 0.003 . 36 7 7 HIS H H 8.540 0.003 1 37 7 7 HIS HA H 4.933 0.001 1 38 7 7 HIS HB2 H 3.204 0.004 2 39 7 7 HIS HB3 H 3.102 0.004 2 40 7 7 HIS HD2 H 7.305 0.002 1 41 7 7 HIS HE1 H 8.246 0.000 1 42 8 8 PRO HA H 4.397 0.003 1 43 8 8 PRO HB2 H 2.220 0.002 2 44 8 8 PRO HB3 H 2.220 0.002 2 45 8 8 PRO HD2 H 3.689 0.005 2 46 8 8 PRO HD3 H 3.526 0.002 2 47 8 8 PRO HG2 H 1.945 0.003 2 48 8 8 PRO HG3 H 1.858 0.005 2 49 9 9 LYS H H 8.567 0.003 1 50 9 9 LYS HA H 4.514 0.004 1 51 9 9 LYS HB2 H 1.833 0.005 2 52 9 9 LYS HB3 H 1.727 0.004 2 53 9 9 LYS HD2 H 1.662 0.000 2 54 9 9 LYS HD3 H 1.662 0.000 2 55 9 9 LYS HG2 H 1.476 0.004 2 56 9 9 LYS HG3 H 1.476 0.004 2 57 10 10 GPR HA H 4.568 0.004 . 58 10 10 GPR HD2 H 3.969 0.002 . 59 10 10 GPR HD3 H 3.603 0.002 . 60 10 10 GPR QB H 2.495 0.004 . 61 10 10 GPR HG11 H 2.035 0.003 . 62 10 10 GPR HG12 H 2.035 0.003 . 63 11 11 ASN H H 8.385 0.004 1 64 11 11 ASN HA H 4.603 0.003 1 65 11 11 ASN HB2 H 2.769 0.002 2 66 11 11 ASN HB3 H 2.728 0.004 2 67 11 11 ASN HD21 H 7.574 0.000 . 68 11 11 ASN HD22 H 7.574 0.000 . 69 12 12 SER H H 7.978 0.001 1 70 12 12 SER HA H 4.266 0.003 1 71 12 12 SER HB2 H 3.665 0.005 2 72 12 12 SER HB3 H 3.665 0.005 2 73 13 13 DPN H H 8.053 0.004 . 74 13 13 DPN HA H 4.573 0.001 . 75 13 13 DPN HB2 H 2.882 0.003 . 76 13 13 DPN HB3 H 2.767 0.000 . 77 14 14 TRP H H 8.278 0.003 1 78 14 14 TRP HA H 4.745 0.003 1 79 14 14 TRP HB2 H 3.288 0.003 2 80 14 14 TRP HB3 H 3.125 0.004 2 81 14 14 TRP HE3 H 7.605 0.001 1 82 15 15 THR H H 8.009 0.003 1 83 15 15 THR HA H 4.242 0.000 1 84 15 15 THR HB H 4.107 0.000 1 85 15 15 THR HG2 H 1.142 0.000 . stop_ save_