data_6941 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; '1H, 13C, and 15N Chemical Shift Assignments for Ac-Dab-Dab-(Ala)7-Orn-Orn-NH2 where Dab-diaminobutyric acid; Orn - ornithine' ; _BMRB_accession_number 6941 _BMRB_flat_file_name bmr6941.str _Entry_type original _Submission_date 2004-01-17 _Accession_date 2004-01-17 _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 Makowska Joanna . . 2 Rodziewicz-Motowidlo Sylwia . . 3 Baginska Katarzyna . . 4 Vila Jorge A. . 5 Liwo Adam . . 6 Chmurzynski Lech K. . 7 Scheraga Harold A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 55 "13C chemical shifts" 28 "15N chemical shifts" 12 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-01-29 original author . stop_ _Original_release_date 2007-01-29 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16446433 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Makowska Joanna . . 2 Rodziewicz-Motowidlo Sylwia . . 3 Baginska Katarzyna . . 4 Vila Jorge A. . 5 Liwo Adam . . 6 Chmurzynski Lech K. . 7 Scheraga Harold A. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_volume 103 _Journal_issue 6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1744 _Page_last 1749 _Year 2006 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name XAO _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'subunit 1' $XAO stop_ _System_molecular_weight 985.5 _System_physical_state unfolded _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details Ac-Dab-Dab-(Ala)7-Orn-Orn-NH2 save_ ######################## # Monomeric polymers # ######################## save_XAO _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common XAO _Molecular_mass 985.5 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence XXAAAAAAAXX loop_ _Residue_seq_code _Residue_label 1 DAB 2 DAB 3 ALA 4 ALA 5 ALA 6 ALA 7 ALA 8 ALA 9 ALA 10 ORN 11 ORN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DAB _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common '2,4-DIAMINOBUTYRIC ACID' _BMRB_code . _PDB_code DAB _Standard_residue_derivative . _Molecular_mass 118.134 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Sep 2 12:08:45 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 . ? ND ND N . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 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 H2 ? ? 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 ND ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING ND HD1 ? ? SING ND HD2 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_ORN _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common L-ornithine _BMRB_code . _PDB_code ORN _Standard_residue_derivative . _Molecular_mass 132.161 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Sep 2 12:10:20 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 . ? CD CD C . 0 . ? NE NE N . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 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 H2 ? ? 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 NE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING NE HE1 ? ? SING NE HE2 ? ? 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 $XAO . . . . . . 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 $XAO 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'The molecule was dissolved in acetate buffer' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $XAO 4 mM . 'sodium acetate buffer' 30 mM . D2O 10 % . H2O 90 % . stop_ save_ ############################ # Computer software used # ############################ save_software_2 _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 1 . http://spin.niddk.nih.gov/NMRPipe/ 2 . http://hugin.ethz.ch/wuthrich/software/xeasy/index.html stop_ loop_ _Task 'NMR data processing' 'peak assignments' stop_ _Details ; F._Delaglio,_S._Grzesiek,_G._W._Vuister,_G._Zhu,_J._Pfeifer_and_A._Bax,_J._Biomol._NMR._6,_277-293_(1995) Bartles_C,_Xia_T,_Billeter_M,_G?nter_P,_W?thrich_K._(1995)_J._Biomol._NMR_5,_1-10. ; save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Varian Unity 500 Plus' _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1D_NMR_1 _Saveframe_category NMR_applied_experiment _Experiment_name 1D_NMR _Sample_label $sample_1 save_ save_1H1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name 1H1H_TOCSY _Sample_label $sample_1 save_ save_1H1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name 1H1H_NOESY _Sample_label $sample_1 save_ save_1H1H_ROESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name 1H1H_ROESY _Sample_label $sample_1 save_ save_1H13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name 1H13C_HSQC _Sample_label $sample_1 save_ save_1H15N_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name 1H15N_HSQC _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_conditions_1 _Saveframe_category sample_conditions _Details ; The XAO peptide was dissolved in 30 mM sodium acetate buffer (pH 4.5 in 10 % D2O). The peptide concentration was 4 mM. All 2D NMR spectra were recorded at 5oC except for the temperature coefficients of the chemical shifts, which were measured throughout the temperature range 5-44 oC. ; loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.5 0.01 pH temperature 298 0.01 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_referencing _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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS C 13 'methyl protons' ppm 0.0 . indirect . . . 0.251449530 $citation_1 $citation_1 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 $citation_1 $citation_1 DSS N 15 'methyl protons' ppm 0.0 . indirect . . . 0.101329118 $citation_1 $citation_1 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_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_2 stop_ loop_ _Experiment_label 1D_NMR 1H1H_TOCSY 1H1H_NOESY 1H1H_ROESY 1H13C_HSQC 1H15N_HSQC stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $conditions_1 _Chem_shift_reference_set_label $chemical_shift_referencing _Mol_system_component_name '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 1 DAB H1 H 2.04 0.012 1 2 1 1 DAB HA H 4.36 0.012 1 3 1 1 DAB HB2 H 2.14 0.012 1 4 1 1 DAB HB3 H 2.05 0.012 1 5 1 1 DAB HG2 H 3.08 0.012 2 6 1 1 DAB HG3 H 3.08 0.012 2 7 1 1 DAB HZ H 7.81 0.012 5 8 1 1 DAB CA C 54.31 0.003 1 9 1 1 DAB CB C 31.50 0.003 1 10 1 1 DAB CG C 39.10 0.003 1 11 1 1 DAB N N 125 0.003 9 12 1 1 DAB H H 8.63 0.012 1 13 2 2 DAB H H 8.85 0.012 1 14 2 2 DAB HA H 4.42 0.012 1 15 2 2 DAB HB2 H 2.17 0.012 1 16 2 2 DAB HB3 H 2.08 0.012 1 17 2 2 DAB HG2 H 3.08 0.012 2 18 2 2 DAB HG3 H 3.08 0.012 2 19 2 2 DAB HZ H 7.81 0.012 5 20 2 2 DAB CA C 53.98 0.003 1 21 2 2 DAB CB C 31.58 0.003 1 22 2 2 DAB CG C 39.10 0.003 1 23 2 2 DAB N N 121.04 0.003 1 24 3 3 ALA H H 8.64 0.012 1 25 3 3 ALA HA H 4.25 0.012 1 26 3 3 ALA HB H 1.39 0.012 1 27 3 3 ALA CA C 52.54 0.003 1 28 3 3 ALA CB C 19.14 0.003 1 29 3 3 ALA N N 124.13 0.003 1 30 4 4 ALA H H 8.55 0.012 1 31 4 4 ALA HA H 4.24 0.012 1 32 4 4 ALA HB H 1.39 0.012 1 33 4 4 ALA CA C 52.54 0.003 1 34 4 4 ALA CB C 19.14 0.003 1 35 4 4 ALA N N 124.56 0.003 1 36 5 5 ALA H H 8.47 0.012 1 37 5 5 ALA HA H 4.23 0.012 1 38 5 5 ALA HB H 1.39 0.012 1 39 5 5 ALA CA C 52.54 0.003 1 40 5 5 ALA CB C 19.14 0.003 1 41 5 5 ALA N N 124.44 0.003 1 42 6 6 ALA H H 8.44 0.012 1 43 6 6 ALA HA H 4.23 0.012 1 44 6 6 ALA HB H 1.39 0.012 1 45 6 6 ALA CA C 52.54 0.003 1 46 6 6 ALA CB C 19.14 0.003 1 47 6 6 ALA N N 124.17 0.003 1 48 7 7 ALA H H 8.40 0.012 1 49 7 7 ALA HA H 4.23 0.012 . 50 7 7 ALA HB H 1.39 0.012 1 51 7 7 ALA CA C 52.54 0.003 1 52 7 7 ALA CB C 19.14 0.003 1 53 7 7 ALA N N 124.04 0.003 1 54 8 8 ALA H H 8.34 0.012 1 55 8 8 ALA HA H 4.24 0.012 1 56 8 8 ALA HB H 1.39 0.012 1 57 8 8 ALA CA C 52.54 0.003 1 58 8 8 ALA CB C 19.14 0.003 1 59 8 8 ALA N N 123.84 0.003 1 60 9 9 ALA H H 8.36 0.012 1 61 9 9 ALA HA H 4.24 0.012 1 62 9 9 ALA HB H 1.39 0.012 1 63 9 9 ALA CA C 52.54 0.003 1 64 9 9 ALA CB C 19.14 0.003 1 65 9 9 ALA N N 124.01 0.003 1 66 10 10 ORN H H 8.51 0.012 1 67 10 10 ORN HA H 4.31 0.012 1 68 10 10 ORN HB2 H 1.87 0.012 1 69 10 10 ORN HB3 H 1.79 0.012 1 70 10 10 ORN HG2 H 1.78 0.012 2 71 10 10 ORN HG3 H 1.78 0.012 2 72 10 10 ORN HD2 H 3.02 0.012 2 73 10 10 ORN HD3 H 3.02 0.012 2 74 10 10 ORN HZ H 7.69 0.012 5 75 10 10 ORN CA C 55.89 0.003 1 76 10 10 ORN CB C 30.68 0.003 1 77 10 10 ORN CG C 26.13 0.003 1 78 10 10 ORN CD C 41.79 0.003 1 79 10 10 ORN N N 121.14 0.003 1 80 11 11 ORN H H 8.63 0.012 1 81 11 11 ORN HA H 4.30 0.012 1 82 11 11 ORN HB2 H 1.88 0.012 1 83 11 11 ORN HB3 H 1.79 0.012 1 84 11 11 ORN HG2 H 1.73 0.012 2 85 11 11 ORN HG3 H 1.72 0.012 2 86 11 11 ORN HD2 H 3.02 0.012 2 87 11 11 ORN HD3 H 3.02 0.012 2 88 11 11 ORN HZ H 7.69 0.012 5 89 11 11 ORN H1 H 7.28 0.012 1 90 11 11 ORN CA C 55.89 0.003 1 91 11 11 ORN CB C 30.68 0.003 1 92 11 11 ORN CG C 26.13 0.003 1 93 11 11 ORN CD C 41.79 0.003 1 94 11 11 ORN N N 125.0 0.003 9 95 11 11 ORN NH2 N 109.45 0.003 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity 7 19 '74,88' stop_ save_