data_6815 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of Retrocyclin-2 in SDS ; _BMRB_accession_number 6815 _BMRB_flat_file_name bmr6815.str _Entry_type original _Submission_date 2005-09-09 _Accession_date 2005-09-29 _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 Daly N. L. . 2 Chen Y.-K. . . 3 Rosengren K. J. . 4 Marx U. C. . 5 Phillips M. L. . 6 Waring A. J. . 7 Wang W. . . 8 Lehrer R. I. . 9 Craik D. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 81 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-24 original BMRB . stop_ _Original_release_date 2005-09-29 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Retrocyclin-2: structural analysis of a potent anti-HIV theta-defensin ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17685559 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Daly N. L. . 2 Chen Y.-K. . . 3 Rosengren K. J. . 4 Marx U. C. . 5 Phillips M. L. . 6 Waring A. J. . 7 Wang W. . . 8 Lehrer R. I. . 9 Craik D. J. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 46 _Journal_issue 35 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9920 _Page_last 9928 _Year 2007 _Details . loop_ _Keyword beta-sheet 'circular peptide' 'laddered disulfide connectivity' stop_ save_ ################################## # Molecular system description # ################################## save_system_Retrocyclin-2 _Saveframe_category molecular_system _Mol_system_name Retrocyclin-2 _Abbreviation_common Retrocyclin-2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Retrocyclin-2 $Retrocyclin-2 stop_ _System_molecular_weight . _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Retrocyclin-2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Retrocyclin-2 _Abbreviation_common Retrocyclin-2 _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ; RRICRCICGRGICRCICG ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 ARG 3 ILE 4 CYS 5 ARG 6 CYS 7 ILE 8 CYS 9 GLY 10 ARG 11 GLY 12 ILE 13 CYS 14 ARG 15 CYS 16 ILE 17 CYS 18 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Retrocyclin-2 Human 10090 Eukaryota Metazoa Homo sapien 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 $Retrocyclin-2 '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 $Retrocyclin-2 0.6 mM . SDS 100 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 3.5 loop_ _Task collection stop_ _Details Bruker save_ save_Xeasy _Saveframe_category software _Name XEASY _Version 1.3.7 loop_ _Task 'data analysis' stop_ _Details 'Eccles et al' save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task 'structure solution' stop_ _Details 'Guntert et al' save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task refinement 'structure solution' stop_ _Details Brunger save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _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_E-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 1 . M pH 3.5 . n/a pressure 1 . atm temperature 310 . 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 'methly protons' ppm . . . . . . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' DQF-COSY E-COSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name Retrocyclin-2 _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 ARG H H 8.546 0.000 . 2 . 1 ARG HA H 4.225 0.000 . 3 . 1 ARG HB2 H 2.002 0.000 . 4 . 1 ARG HG2 H 1.818 0.000 . 5 . 2 ARG H H 8.583 0.007 . 6 . 2 ARG HA H 4.538 0.000 . 7 . 2 ARG HB3 H 1.990 0.000 . 8 . 2 ARG HB2 H 1.975 0.000 . 9 . 2 ARG HG2 H 1.704 0.000 . 10 . 3 ILE H H 7.585 0.002 . 11 . 3 ILE HA H 4.538 0.006 . 12 . 3 ILE HB H 1.921 0.003 . 13 . 3 ILE HG2 H 0.963 0.000 . 14 . 3 ILE HG12 H 1.264 0.000 . 15 . 3 ILE HG13 H 1.589 0.000 . 16 . 4 CYS H H 8.444 0.003 . 17 . 4 CYS HA H 5.911 0.001 . 18 . 4 CYS HB2 H 3.067 0.001 . 19 . 4 CYS HB3 H 3.280 0.000 . 20 . 5 ARG H H 8.967 0.005 . 21 . 5 ARG HA H 4.790 0.006 . 22 . 5 ARG HB2 H 1.875 0.000 . 23 . 5 ARG HB3 H 1.971 0.000 . 24 . 5 ARG HG2 H 1.722 0.000 . 25 . 6 CYS H H 8.656 0.000 . 26 . 6 CYS HA H 5.576 0.000 . 27 . 6 CYS HB2 H 2.808 0.006 . 28 . 6 CYS HB3 H 3.164 0.001 . 29 . 7 ILE H H 9.024 0.003 . 30 . 7 ILE HA H 4.637 0.003 . 31 . 7 ILE HB H 1.886 0.005 . 32 . 7 ILE HG2 H 1.014 0.002 . 33 . 7 ILE HG12 H 1.280 0.000 . 34 . 7 ILE HG13 H 1.645 0.000 . 35 . 8 CYS H H 8.252 0.004 . 36 . 8 CYS HA H 5.942 0.005 . 37 . 8 CYS HB2 H 2.958 0.008 . 38 . 8 CYS HB3 H 3.142 0.009 . 39 . 9 GLY H H 8.911 0.003 . 40 . 9 GLY HA2 H 3.745 0.004 . 41 . 9 GLY HA3 H 4.343 0.009 . 42 . 10 ARG H H 8.806 0.002 . 43 . 10 ARG HA H 4.009 0.003 . 44 . 10 ARG HB2 H 2.211 0.006 . 45 . 10 ARG HB3 H 2.024 0.000 . 46 . 10 ARG HG2 H 1.776 0.000 . 47 . 11 GLY H H 8.471 0.003 . 48 . 11 GLY HA2 H 3.735 0.006 . 49 . 11 GLY HA3 H 4.233 0.004 . 50 . 12 ILE H H 8.109 0.001 . 51 . 12 ILE HA H 4.516 0.001 . 52 . 12 ILE HB H 2.115 0.008 . 53 . 12 ILE HG2 H 1.003 0.006 . 54 . 12 ILE HG12 H 1.278 0.000 . 55 . 12 ILE HG13 H 1.621 0.000 . 56 . 13 CYS H H 8.413 0.002 . 57 . 13 CYS HA H 5.854 0.006 . 58 . 13 CYS HB2 H 2.868 0.000 . 59 . 13 CYS HB3 H 2.976 0.084 . 60 . 14 ARG H H 9.168 0.001 . 61 . 14 ARG HA H 4.780 0.006 . 62 . 14 ARG HB2 H 1.805 0.000 . 63 . 14 ARG HB3 H 1.898 0.000 . 64 . 14 ARG HG2 H 1.683 0.000 . 65 . 15 CYS H H 8.719 0.000 . 66 . 15 CYS HA H 5.503 0.000 . 67 . 15 CYS HB2 H 2.951 0.000 . 68 . 15 CYS HB3 H 3.154 0.000 . 69 . 16 ILE H H 8.705 0.002 . 70 . 16 ILE HA H 4.571 0.000 . 71 . 16 ILE HB H 1.898 0.000 . 72 . 16 ILE HG2 H 1.018 0.000 . 73 . 16 ILE HG12 H 1.257 0.000 . 74 . 16 ILE HG13 H 1.663 0.000 . 75 . 17 CYS H H 8.677 0.006 . 76 . 17 CYS HA H 5.582 0.003 . 77 . 17 CYS HB2 H 2.972 0.000 . 78 . 17 CYS HB3 H 3.312 0.007 . 79 . 18 GLY H H 8.717 0.005 . 80 . 18 GLY HA2 H 4.082 0.001 . 81 . 18 GLY HA3 H 4.600 0.001 . stop_ save_