data_25004 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shift assignments for the parallel in-register D23N Iowa Mutant Beta Amyloid Fibrils ; _BMRB_accession_number 25004 _BMRB_flat_file_name bmr25004.str _Entry_type original _Submission_date 2014-06-07 _Accession_date 2014-06-07 _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 Sgourakis Nikolaos . . 2 Qiang Wei . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 59 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-04-20 original BMRB . stop_ _Original_release_date 2015-04-20 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Modeling an in-register, parallel "iowa" a beta fibril structure using solid-state NMR data from labeled samples with rosetta ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25543257 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sgourakis Nikolaos . . 2 Yau Wai-Ming . . 3 Qiang Wei . . stop_ _Journal_abbreviation Structure _Journal_volume 23 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 216 _Page_last 227 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name D23N_parallel _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label D23N_Abeta $D23N_Abeta stop_ _System_molecular_weight . _System_physical_state misfolded _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_D23N_Abeta _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common D23N_Abeta _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 26 _Mol_residue_sequence ; QKLVFFAENVGSNKGAIIGL MVGGVV ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 15 GLN 2 16 LYS 3 17 LEU 4 18 VAL 5 19 PHE 6 20 PHE 7 21 ALA 8 22 GLU 9 23 ASN 10 24 VAL 11 25 GLY 12 26 SER 13 27 ASN 14 28 LYS 15 29 GLY 16 30 ALA 17 31 ILE 18 32 ILE 19 33 GLY 20 34 LEU 21 35 MET 22 36 VAL 23 37 GLY 24 38 GLY 25 39 VAL 26 40 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-06-02 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 17774 entity 100.00 26 100.00 100.00 5.34e-07 BMRB 18175 entity 100.00 26 100.00 100.00 5.34e-07 PDB 2LNQ "40-residue D23n Beta Amyloid Fibril" 100.00 40 100.00 100.00 2.52e-07 PDB 2MPZ 'Atomic Model Of The Abeta D23n "iowa" Mutant Using Solid-state Nmr, Em And Rosetta Modeling' 100.00 26 100.00 100.00 5.34e-07 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $D23N_Abeta Human 9606 Eukaryota Metazoa Homo sapiens 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 $D23N_Abeta 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_D23N_parallel _Saveframe_category sample _Sample_type 'gel solid' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $D23N_Abeta . uM 25 100 '[U-100% 13C; U-100% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_NA _Saveframe_category software _Name NA _Version . loop_ _Vendor _Address _Electronic_address NA . . stop_ loop_ _Task NA stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 400 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_spin_diffusion_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C spin diffusion' _Sample_label $D23N_parallel save_ save_1D_13C_PITHIRDs_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 13C PITHIRDs' _Sample_label $D23N_parallel save_ save_1D_13C-15N_REDOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 13C-15N REDOR' _Sample_label $D23N_parallel save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 10 . mM pH 7.4 . pH pressure . . atm temperature 298 . 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 Alanine C 13 'carbonyl carbon' ppm 177.95 external direct . . . 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 13C-13C spin diffusion' stop_ loop_ _Sample_label $D23N_parallel stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name D23N_Abeta _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 16 2 LYS C C 172.9 . . 2 16 2 LYS CA C 52.2 . . 3 16 2 LYS CB C 34.5 . . 4 17 3 LEU C C 175.1 . . 5 17 3 LEU CA C 52.0 . . 6 17 3 LEU CB C 43.1 . . 7 19 5 PHE C C 173.8 . . 8 19 5 PHE CA C 52.9 . . 9 19 5 PHE CB C 41.9 . . 10 20 6 PHE C C 173.6 . . 11 20 6 PHE CA C 52.8 . . 12 20 6 PHE CB C 42.7 . . 13 21 7 ALA C C 175.0 . . 14 21 7 ALA CA C 48.0 . . 15 21 7 ALA CB C 21.3 . . 16 22 8 GLU C C 174.5 . . 17 22 8 GLU CA C 57.6 . . 18 22 8 GLU CB C 29.1 . . 19 23 9 ASN C C 173.8 . . 20 23 9 ASN CA C 51.0 . . 21 23 9 ASN CB C 41.4 . . 22 24 10 VAL C C 174.8 . . 23 24 10 VAL CA C 60.8 . . 24 24 10 VAL CB C 33.4 . . 25 28 14 LYS C C 174.8 . . 26 28 14 LYS CA C 55.9 . . 27 28 14 LYS CB C 29.2 . . 28 29 15 GLY C C 171.2 . . 29 29 15 GLY CA C 43.8 . . 30 30 16 ALA C C 174.7 . . 31 30 16 ALA CA C 47.3 . . 32 30 16 ALA CB C 19.2 . . 33 31 17 ILE C C 174.0 . . 34 31 17 ILE CA C 57.2 . . 35 31 17 ILE CB C 38.8 . . 36 32 18 ILE C C 173.9 . . 37 32 18 ILE CA C 56.1 . . 38 32 18 ILE CB C 40.5 . . 39 33 19 GLY C C 170.9 . . 40 33 19 GLY CA C 42.4 . . 41 34 20 LEU C C 174.8 . . 42 34 20 LEU CA C 51.6 . . 43 34 20 LEU CB C 43.6 . . 44 35 21 MET C C 172.7 . . 45 35 21 MET CA C 51.3 . . 46 35 21 MET CB C 34.0 . . 47 36 22 VAL C C 174.4 . . 48 36 22 VAL CA C 58.3 . . 49 36 22 VAL CB C 33.0 . . 50 37 23 GLY C C 171.4 . . 51 37 23 GLY CA C 43.7 . . 52 38 24 GLY C C 169.7 . . 53 38 24 GLY CA C 42.3 . . 54 39 25 VAL C C 172.9 . . 55 39 25 VAL CA C 58.2 . . 56 39 25 VAL CB C 32.4 . . 57 40 26 VAL C C 169.0 . . 58 40 26 VAL CA C 60.0 . . 59 40 26 VAL CB C 33.9 . . stop_ save_