data_6511 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of peptide SD ; _BMRB_accession_number 6511 _BMRB_flat_file_name bmr6511.str _Entry_type original _Submission_date 2005-02-17 _Accession_date 2005-02-18 _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 Murata T. . . 2 Hemmi H. . . 3 Nakamura S. . . 4 Shimizu K. . . 5 Suzuki Y. . . 6 Yamaguchi I. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 52 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2005-09-22 original BMRB . stop_ _Original_release_date 2005-02-18 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure, epitope mapping and docking simulation of a gibberellin mimic peptide recognized by an anti-gibberellin A4 antibody 4-B8(8)/E9 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Murata T. . . 2 Hemmi H. . . 3 Nakamura S. . . 4 Shimizu K. . . 5 Suzuki Y. . . 6 Yamaguchi I. . . stop_ _Journal_abbreviation 'FEBS J.' _Journal_volume 272 _Journal_issue 19 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4938 _Page_last 4948 _Year 2005 _Details . loop_ _Keyword STD-NMR gibberellin mimic stop_ save_ ################################## # Molecular system description # ################################## save_system_SD _Saveframe_category molecular_system _Mol_system_name 'peptide SD' _Abbreviation_common SD _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'peptide SD' $SD_monomer stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SD_monomer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'peptide SD' _Abbreviation_common SD _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; ACLPWSDGPC ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 CYS 3 LEU 4 PRO 5 TRP 6 SER 7 ASP 8 GLY 9 PRO 10 CYS stop_ _Sequence_homology_query_date 2005-11-24 _Sequence_homology_query_revised_last_date 2005-10-21 save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $SD_monomer 'not applicable' . . . . . 'gibberellin mimic peptide' 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 $SD_monomer '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 $SD_monomer 5 mM . 'phosphate buffer' 50 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 2.6 loop_ _Task collection processing stop_ _Details Bruker save_ save_Sparky _Saveframe_category software _Name SPARKY _Version 3 loop_ _Task 'data analysis' stop_ _Details 'Goddard and Kneller' save_ save_CNS _Saveframe_category software _Name CNS _Version 1.0 loop_ _Task refinement stop_ _Details Brunger save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _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_2D_ROESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ROESY' _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 pH 5.0 0.05 pH pressure 1 . atm temperature 298 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' '2D TOCSY' DQF-COSY '2D ROESY' 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 'peptide SD' _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 ALA HA H 4.10 0.01 1 2 . 1 ALA HB H 1.50 0.01 1 3 . 2 CYS H H 8.76 0.01 1 4 . 2 CYS HA H 4.68 0.01 1 5 . 2 CYS HB2 H 2.95 0.01 1 6 . 2 CYS HB3 H 3.12 0.01 1 7 . 3 LEU H H 8.65 0.01 1 8 . 3 LEU HA H 4.52 0.01 1 9 . 3 LEU HB2 H 1.23 0.01 1 10 . 3 LEU HB3 H 0.72 0.01 1 11 . 3 LEU HG H 1.56 0.01 1 12 . 3 LEU HD1 H 0.85 0.01 2 13 . 3 LEU HD2 H 0.92 0.01 2 14 . 4 PRO HA H 4.24 0.01 1 15 . 4 PRO HB2 H 1.80 0.01 2 16 . 4 PRO HB3 H 2.20 0.01 2 17 . 4 PRO HG2 H 1.95 0.01 1 18 . 4 PRO HG3 H 2.00 0.01 1 19 . 4 PRO HD2 H 3.21 0.01 2 20 . 4 PRO HD3 H 3.69 0.01 2 21 . 5 TRP H H 7.04 0.01 1 22 . 5 TRP HA H 4.74 0.01 1 23 . 5 TRP HB2 H 3.33 0.01 2 24 . 5 TRP HB3 H 3.49 0.01 2 25 . 5 TRP HD1 H 7.22 0.01 1 26 . 5 TRP HE1 H 10.31 0.01 1 27 . 5 TRP HE3 H 7.67 0.01 1 28 . 5 TRP HZ2 H 7.55 0.01 1 29 . 5 TRP HZ3 H 7.23 0.01 1 30 . 5 TRP HH2 H 7.30 0.01 1 31 . 6 SER H H 7.62 0.01 1 32 . 6 SER HA H 4.42 0.01 1 33 . 6 SER HB2 H 3.77 0.01 1 34 . 6 SER HB3 H 3.77 0.01 1 35 . 7 ASP H H 8.48 0.01 1 36 . 7 ASP HA H 4.77 0.01 1 37 . 7 ASP HB2 H 2.74 0.01 2 38 . 7 ASP HB3 H 2.81 0.01 2 39 . 8 GLY H H 7.92 0.01 1 40 . 8 GLY HA2 H 4.05 0.01 2 41 . 8 GLY HA3 H 4.12 0.01 2 42 . 9 PRO HA H 4.43 0.01 1 43 . 9 PRO HB2 H 2.25 0.01 2 44 . 9 PRO HB3 H 1.93 0.01 2 45 . 9 PRO HG2 H 2.01 0.01 1 46 . 9 PRO HG3 H 2.01 0.01 1 47 . 9 PRO HD2 H 3.60 0.01 1 48 . 9 PRO HD3 H 3.60 0.01 1 49 . 10 CYS H H 8.16 0.01 1 50 . 10 CYS HA H 4.44 0.01 1 51 . 10 CYS HB2 H 3.06 0.01 1 52 . 10 CYS HB3 H 3.19 0.01 1 stop_ save_