data_6101 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of a D,L-Alternating Oligonorleucine as a Model of Double-Stranded Antiparallel beta-helix ; _BMRB_accession_number 6101 _BMRB_flat_file_name bmr6101.str _Entry_type original _Submission_date 2004-02-19 _Accession_date 2004-02-19 _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 Navarro E. . . 2 Fennude E. . . 3 Celda B. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 85 "13C chemical shifts" 15 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-08-11 update BMRB 'Updating non-standard residue' 2008-07-11 update BMRB 'Updating non-standard residue' 2008-03-24 update BMRB . 2004-05-15 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution Structure of a D,L-Alternating Oligonorleucine as a Model of Double-Stranded Antiparallel beta-helix' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12115137 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Navarro E. . . 2 Fennude E. . . 3 Celda B. . . stop_ _Journal_abbreviation Biopolymers _Journal_volume 64 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 198 _Page_last 209 _Year 2002 _Details . loop_ _Keyword beta-helix d,l-alternating gramicidin norleucine stop_ save_ ################################## # Molecular system description # ################################## save_system_ESTER _Saveframe_category molecular_system _Mol_system_name 'BOC-L-NLE-(D-NLE-L-NLE)5-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER' _Abbreviation_common 'METHYL ESTER' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'METHYL ESTER chain A' $METHYL_ESTER 'METHYL ESTER chain B' $METHYL_ESTER stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_METHYL_ESTER _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'METHYL ESTER' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence XXXXXXXXXXXXXXX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 NLE 2 2 DNE 3 3 NLE 4 4 DNE 5 5 NLE 6 6 DNE 7 7 NLE 8 8 DNE 9 9 NLE 10 10 DNE 11 11 NLE 12 12 DNM 13 13 NLE 14 14 DNE 15 15 NLE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NLE _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common NORLEUCINE _BMRB_code . _PDB_code NLE _Standard_residue_derivative . _Molecular_mass 131.173 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 3 15:46:34 2012 ; 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 . ? CD CD C . 0 . ? CE CE C . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HXT HXT 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 . ? HE3 HE3 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 HN2 ? ? 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 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE HE1 ? ? SING CE HE2 ? ? SING CE HE3 ? ? stop_ save_ save_chem_comp_DNE _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-NORLEUCINE _BMRB_code . _PDB_code DNE _Standard_residue_derivative . _Molecular_mass 131.173 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 3 15:48:24 2012 ; 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 . ? CD CD C . 0 . ? CE CE C . 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 . ? HE3 HE3 H . 0 . ? HO1 HO1 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 CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE HE1 ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING OXT HO1 ? ? stop_ save_ save_chem_comp_DNM _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common N-METHYL-D-NORLEUCINE _BMRB_code . _PDB_code DNM _Standard_residue_derivative . _Molecular_mass 145.199 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 3 15:49:50 2012 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? OXT OXT O . 0 . ? HC1 HC1 H . 0 . ? HC2 HC2 H . 0 . ? HC3 HC3 H . 0 . ? H H 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 . ? HE3 HE3 H . 0 . ? HO1 HO1 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 C1 N ? ? SING C1 HC1 ? ? SING C1 HC2 ? ? SING C1 HC3 ? ? SING N CA ? ? SING N H ? ? 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 CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE HE1 ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING OXT HO1 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $METHYL_ESTER . . . . . . 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 $METHYL_ESTER '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 $METHYL_ESTER 4.7 mM . stop_ save_ ############################ # Computer software used # ############################ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 2.9.7 loop_ _Task refinement 'structure solution' stop_ _Details BIOSYM save_ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Task 'data analysis' stop_ _Details VARIAN save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UNITY _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_ROESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ROESY' _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pressure 1 . atm temperature 303 . 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 TMS C 13 . ppm . . . . . . TMS H 1 . ppm . . . . . . 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_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'METHYL ESTER chain A' _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 NLE H H 6.41 . 1 2 1 1 NLE HA H 4.23 . 1 3 1 1 NLE HB2 H 1.70 . 2 4 1 1 NLE HG2 H 1.95 . 2 5 1 1 NLE HD2 H 1.31 . 2 6 1 1 NLE HE1 H 0.86 . 2 7 1 1 NLE CA C 54.3 . 1 8 2 2 DNE H H 7.67 . 1 9 2 2 DNE HA H 4.83 . 1 10 2 2 DNE HB2 H 1.82 . 2 11 2 2 DNE HD2 H 1.31 . 2 12 2 2 DNE HE1 H 0.88 . 2 13 2 2 DNE CA C 52.6 . 1 14 3 3 NLE H H 8.30 . 1 15 3 3 NLE HA H 4.99 . 1 16 3 3 NLE HB2 H 1.59 . 2 17 3 3 NLE HG2 H 1.73 . 2 18 3 3 NLE HD2 H 1.35 . 2 19 3 3 NLE HE1 H 0.86 . 2 20 3 3 NLE CA C 50.1 . 1 21 4 4 DNE H H 8.60 . 1 22 4 4 DNE HA H 4.73 . 1 23 4 4 DNE HB2 H 1.49 . 2 24 4 4 DNE HD2 H 1.25 . 2 25 4 4 DNE HE1 H 0.88 . 2 26 4 4 DNE CA C 51.2 . 1 27 5 5 NLE H H 8.70 . 1 28 5 5 NLE HA H 4.79 . 1 29 5 5 NLE HB2 H 1.60 . 2 30 5 5 NLE HG2 H 1.66 . 2 31 5 5 NLE HD2 H 1.30 . 2 32 5 5 NLE HE1 H 0.86 . 2 33 5 5 NLE CA C 50.9 . 1 34 6 6 DNE H H 8.60 . 1 35 6 6 DNE HA H 4.84 . 1 36 6 6 DNE HB2 H 1.70 . 2 37 6 6 DNE HD2 H 1.28 . 2 38 6 6 DNE HE1 H 0.86 . 2 39 6 6 DNE CA C 51.9 . 1 40 7 7 NLE H H 9.14 . 1 41 7 7 NLE HA H 5.00 . 1 42 7 7 NLE HB2 H 1.61 . 2 43 7 7 NLE HG2 H 1.64 . 2 44 7 7 NLE HD2 H 1.30 . 2 45 7 7 NLE HE1 H 0.85 . 2 46 7 7 NLE CA C 50.6 . 1 47 8 8 DNE H H 8.50 . 1 48 8 8 DNE HA H 4.77 . 1 49 8 8 DNE HB2 H 1.72 . 2 50 8 8 DNE HG2 H 1.71 . 2 51 8 8 DNE HD2 H 1.26 . 2 52 8 8 DNE HE1 H 0.91 . 2 53 8 8 DNE CA C 52.2 . 1 54 9 9 NLE H H 9.14 . 1 55 9 9 NLE HA H 4.56 . 1 56 9 9 NLE HB2 H 1.76 . 2 57 9 9 NLE HG2 H 1.69 . 2 58 9 9 NLE HD2 H 1.40 . 2 59 9 9 NLE HE1 H 0.88 . 2 60 9 9 NLE CA C 51.4 . 1 61 10 10 DNE H H 8.29 . 1 62 10 10 DNE HA H 4.95 . 1 63 10 10 DNE HB2 H 1.92 . 2 64 10 10 DNE HG2 H 1.80 . 2 65 10 10 DNE HD2 H 1.23 . 2 66 10 10 DNE CA C 52.4 . 1 67 11 11 NLE H H 9.02 . 1 68 11 11 NLE HA H 4.96 . 1 69 11 11 NLE HB2 H 1.51 . 2 70 11 11 NLE HG2 H 1.54 . 2 71 11 11 NLE HD2 H 1.28 . 2 72 11 11 NLE HE1 H 0.84 . 2 73 11 11 NLE CA C 47.9 . 1 74 12 12 DNM HA H 5.09 . 1 75 12 12 DNM HB2 H 1.90 . 2 76 12 12 DNM HG2 H 1.44 . 2 77 12 12 DNM HD2 H 1.25 . 2 78 12 12 DNM HD3 H 1.19 . 2 79 12 12 DNM HE1 H 0.86 . 2 80 12 12 DNM CA C 55.9 . 1 81 13 13 NLE H H 9.35 . 1 82 13 13 NLE HA H 4.47 . 1 83 13 13 NLE HB2 H 1.66 . 2 84 13 13 NLE HG2 H 1.72 . 2 85 13 13 NLE HD2 H 1.30 . 2 86 13 13 NLE HE1 H 0.88 . 2 87 13 13 NLE CA C 52.0 . 1 88 14 14 DNE H H 6.67 . 1 89 14 14 DNE HA H 4.90 . 1 90 14 14 DNE HB2 H 1.77 . 2 91 14 14 DNE HD2 H 1.32 . 2 92 14 14 DNE HE1 H 0.88 . 2 93 14 14 DNE CA C 52.5 . 1 94 15 15 NLE H H 8.44 . 1 95 15 15 NLE HA H 4.50 . 1 96 15 15 NLE HB2 H 1.76 . 2 97 15 15 NLE HG2 H 1.86 . 2 98 15 15 NLE HD2 H 1.38 . 2 99 15 15 NLE HE1 H 0.91 . 2 100 15 15 NLE CA C 51.3 . 1 stop_ save_