data_20050 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR STRUCTURE OF DPAKKR, A CYCLIC PENTAPEPTIDE MIMIC OF BDNF ; _BMRB_accession_number 20050 _BMRB_flat_file_name bmr20050.str _Entry_type original _Submission_date 2008-10-13 _Accession_date 2008-10-13 _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 Morton Craig J. . 2 Hughes Richard A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 39 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-02-14 update BMRB 'PDBj annotated the coordinate file' 2009-04-04 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Design of a conformationally defined and proteolytically stable circular mimetic of brain-derived neurotrophic factor' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18809686 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Fletcher Jordan M. . 2 Morton Craig J. . 3 Zwar Richard A. . 4 Murray Simon S. . 5 O'Leary Paul D. . 6 Hughes Richard A. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 283 _Journal_issue 48 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 33375 _Page_last 33383 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'D-PAKKR monomer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'D-PAKKR monomer' $D-PAKKR stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'Monomer of the cyclised pentapeptide D-PAKKR' save_ ######################## # Monomeric polymers # ######################## save_D-PAKKR _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common D-PAKKR _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 5 _Mol_residue_sequence XAKKR loop_ _Residue_seq_code _Residue_label 1 DPR 2 ALA 3 LYS 4 LYS 5 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DPR _Saveframe_category polymer_residue _Mol_type 'D-peptide linking' _Name_common D-PROLINE _BMRB_code . _PDB_code DPR _Standard_residue_derivative DPR _Molecular_mass 115.130 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 15 18:42:06 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C N 0 . ? CA CA C R 0 . ? CB CB C N 0 . ? CD CD C N 0 . ? CG CG C N 0 . ? H H H N 0 . ? HA HA H N 0 . ? HB2 HB2 H N 0 . ? HB3 HB3 H N 0 . ? HD2 HD2 H N 0 . ? HD3 HD3 H N 0 . ? HG2 HG2 H N 0 . ? HG3 HG3 H N 0 . ? HXT HXT H N 0 . ? N N N N 0 . ? O O O N 0 . ? OXT OXT O N 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 CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD HD2 ? ? SING CD HD3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $D-PAKKR . . . . . . 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 $D-PAKKR 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'pH adjusted to 5.2' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $D-PAKKR 2-5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_ROESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.2 . pH temperature 288 . 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 TOCSY' '2D DQF-COSY' '2D 1H-1H ROESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'D-PAKKR monomer' _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 DPR HA H 4.32 0.01 1 2 1 1 DPR HB2 H 1.96 0.01 2 3 1 1 DPR HB3 H 2.17 0.01 2 4 1 1 DPR HD2 H 2.68 0.01 2 5 1 1 DPR HD3 H 3.55 0.01 2 6 1 1 DPR HG2 H 1.97 0.01 2 7 1 1 DPR HG3 H 2.15 0.01 2 8 2 2 ALA H H 8.9 0.01 1 9 2 2 ALA HA H 4.21 0.01 1 10 2 2 ALA HB H 1.4 0.01 1 11 3 3 LYS H H 7.79 0.01 1 12 3 3 LYS HA H 4.5 0.01 1 13 3 3 LYS HB2 H 1.8 0.01 2 14 3 3 LYS HB3 H 1.96 0.01 2 15 3 3 LYS HD2 H 1.67 0.01 2 16 3 3 LYS HD3 H 1.67 0.01 2 17 3 3 LYS HE2 H 2.94 0.01 2 18 3 3 LYS HE3 H 2.94 0.01 2 19 3 3 LYS HG2 H 1.31 0.01 2 20 3 3 LYS HG3 H 1.4 0.01 2 21 4 4 LYS H H 7.93 0.01 1 22 4 4 LYS HA H 3.98 0.01 1 23 4 4 LYS HB2 H 1.85 0.01 2 24 4 4 LYS HB3 H 1.85 0.01 2 25 4 4 LYS HD2 H 1.66 0.01 2 26 4 4 LYS HD3 H 1.66 0.01 2 27 4 4 LYS HE2 H 2.94 0.01 2 28 4 4 LYS HE3 H 2.94 0.01 2 29 4 4 LYS HG2 H 1.4 0.01 2 30 4 4 LYS HG3 H 1.45 0.01 2 31 5 5 ARG H H 7.73 0.01 1 32 5 5 ARG HA H 4.54 0.01 1 33 5 5 ARG HB2 H 1.51 0.01 2 34 5 5 ARG HB3 H 1.77 0.01 2 35 5 5 ARG HD2 H 3.19 0.01 2 36 5 5 ARG HD3 H 3.19 0.01 2 37 5 5 ARG HE H 7.2 0.01 1 38 5 5 ARG HG2 H 1.62 0.01 2 39 5 5 ARG HG3 H 1.62 0.01 2 stop_ save_