data_19767 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solid-state NMR assignment of metal-free SOD1 fibrillar structures ; _BMRB_accession_number 19767 _BMRB_flat_file_name bmr19767.str _Entry_type original _Submission_date 2014-02-05 _Accession_date 2014-02-05 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'In this construct residues 49 81 and 124 139 of SOD1 were replaced with a short Gly-Ala-Gly tripeptide linkers.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Banci Lucia . . 2 Blazevits Olga . . 3 Cantini Francesca . . 4 Danielsson Jens . . 5 Lang Lisa . . 6 Luchinat Claudio . . 7 Mao Jiafei . . 8 Oliveberg Mikael . . 9 Ravera Enrico . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 79 "15N chemical shifts" 28 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-06-05 original author . stop_ _Original_release_date 2014-06-05 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solid-state NMR studies of metal-free SOD1 fibrillar structures.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24719206 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Banci Lucia . . 2 Blaevit Olga . . 3 Cantini Francesca . . 4 Danielsson Jens . . 5 Lang Lisa . . 6 Luchinat Claudio . . 7 Mao Jiafei . . 8 Oliveberg Mikael . . 9 Ravera Enrico . . stop_ _Journal_abbreviation 'J. Biol. Inorg. Chem.' _Journal_name_full 'Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry' _Journal_volume 19 _Journal_issue 4-5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 659 _Page_last 666 _Year 2014 _Details . loop_ _Keyword ALS FIBRILS SOD1 'SOLID STATE NMR' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name fibrils _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label apoSOD1-DeltaIV-VII $apoSOD1-DeltaIV-VII stop_ _System_molecular_weight . _System_physical_state na _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'fibrils of apoSOD1-DeltaIV-VII' save_ ######################## # Monomeric polymers # ######################## save_apoSOD1-DeltaIV-VII _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common apoSOD1-DeltaIV-VII _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 110 _Mol_residue_sequence ; ATKAVAVLKGDGPVQGIINF EQKESNGPVKVWGSIKGLTE GLHGFHVHGAGGDLGNVTAD KDGVADVSIEDSVISLSGDH SIIGRTLVVHEKAGAGAGSR LASGVIGIAQ ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ALA 2 2 THR 3 3 LYS 4 4 ALA 5 5 VAL 6 6 ALA 7 7 VAL 8 8 LEU 9 9 LYS 10 10 GLY 11 11 ASP 12 12 GLY 13 13 PRO 14 14 VAL 15 15 GLN 16 16 GLY 17 17 ILE 18 18 ILE 19 19 ASN 20 20 PHE 21 21 GLU 22 22 GLN 23 23 LYS 24 24 GLU 25 25 SER 26 26 ASN 27 27 GLY 28 28 PRO 29 29 VAL 30 30 LYS 31 31 VAL 32 32 TRP 33 33 GLY 34 34 SER 35 35 ILE 36 36 LYS 37 37 GLY 38 38 LEU 39 39 THR 40 40 GLU 41 41 GLY 42 42 LEU 43 43 HIS 44 44 GLY 45 45 PHE 46 46 HIS 47 47 VAL 48 48 HIS 49 49 GLY 50 50 ALA 51 51 GLY 52 52 GLY 53 53 ASP 54 54 LEU 55 55 GLY 56 56 ASN 57 57 VAL 58 58 THR 59 59 ALA 60 60 ASP 61 61 LYS 62 62 ASP 63 63 GLY 64 64 VAL 65 65 ALA 66 66 ASP 67 67 VAL 68 68 SER 69 69 ILE 70 70 GLU 71 71 ASP 72 72 SER 73 73 VAL 74 74 ILE 75 75 SER 76 76 LEU 77 77 SER 78 78 GLY 79 79 ASP 80 80 HIS 81 81 SER 82 82 ILE 83 83 ILE 84 84 GLY 85 85 ARG 86 86 THR 87 87 LEU 88 88 VAL 89 89 VAL 90 90 HIS 91 91 GLU 92 92 LYS 93 93 ALA 94 94 GLY 95 95 ALA 96 96 GLY 97 97 ALA 98 98 GLY 99 99 SER 100 100 ARG 101 101 LEU 102 102 ALA 103 103 SER 104 104 GLY 105 105 VAL 106 106 ILE 107 107 GLY 108 108 ILE 109 109 ALA 110 110 GLN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-09 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 PDB 4BCZ "Monomeric Human Cu,zn Superoxide Dismutase, Loops Iv And Vii Deleted, Apo Form" 100.00 110 100.00 100.00 8.62e-68 PDB 4BD4 "Monomeric Human Cu,zn Superoxide Dismutase, Loops Iv And Vii Deleted, Apo Form, Mutant H43f" 100.00 110 99.09 99.09 9.70e-67 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $apoSOD1-DeltaIV-VII . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Variant _Vector_name $apoSOD1-DeltaIV-VII 'recombinant technology' . Escherichia coli Origami pLysS pET3a stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type fiber _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling apoSOD1-DeltaIV-VII na na '[U-13C; U-15N]' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_CARA _Saveframe_category software _Name CARA _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 850 _Details 'wide-bore instrument operating at 20.0 T' save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DARR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DARR' _Sample_label $sample_1 save_ save_2D_NCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NCA' _Sample_label $sample_1 save_ save_2D_NCO_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NCO' _Sample_label $sample_1 save_ save_3D_NCACX_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NCACX' _Sample_label $sample_1 save_ save_3D_NCOCX_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D NCOCX' _Sample_label $sample_1 save_ save_1H-13C_INEPT-HETCOR_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C INEPT-HETCOR' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'SOD1(IV-VII) fibrils were prepared diluting freshly prepared 13C-15N SOD1(IV-VII) at 200-230 M concentration in 10mM Bis-Tris, pH 6.2 up to the final volume of 10 ml. The obtained solution was incubated at 37 C for 4 days with shaking at 1200 rpm in order to get well mature fibrils' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.2 . pH pressure 1 . 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 TSP C 13 'methyl carbons' ppm 0 external direct . . . 1 '[15N] ammonium chloride' N 15 nitrogen ppm 32.5 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 NCA' 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 apoSOD1-DeltaIV-VII _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 19 19 ASN C C 177.114 0.3 1 2 19 19 ASN CA C 53.005 0.3 1 3 19 19 ASN CB C 38.672 0.3 1 4 19 19 ASN N N 114.809 0.3 1 5 20 20 PHE C C 173.384 0.3 1 6 20 20 PHE CA C 57.185 0.3 1 7 20 20 PHE CB C 42.296 0.3 1 8 20 20 PHE N N 126.203 0.3 1 9 21 21 GLU C C 174.830 0.3 1 10 21 21 GLU CA C 54.722 0.3 1 11 21 21 GLU CB C 33.756 0.3 1 12 21 21 GLU N N 131.884 0.3 1 13 28 28 PRO C C 176.207 0.3 1 14 28 28 PRO CA C 62.646 0.3 1 15 28 28 PRO CB C 31.863 0.3 1 16 29 29 VAL CA C 60.655 0.3 1 17 29 29 VAL CB C 35.545 0.3 1 18 29 29 VAL N N 124.011 0.3 1 19 33 33 GLY C C 171.987 0.3 1 20 33 33 GLY CA C 48.172 0.3 1 21 33 33 GLY N N 120.977 0.3 1 22 34 34 SER C C 172.188 0.3 1 23 34 34 SER CA C 57.334 0.3 1 24 34 34 SER CB C 67.579 0.3 1 25 34 34 SER N N 108.581 0.3 1 26 35 35 ILE C C 175.215 0.3 1 27 35 35 ILE CA C 60.083 0.3 1 28 35 35 ILE CB C 42.132 0.3 1 29 35 35 ILE N N 120.180 0.3 1 30 36 36 LYS C C 175.185 0.3 1 31 36 36 LYS CA C 54.764 0.3 1 32 36 36 LYS CB C 35.757 0.3 1 33 36 36 LYS N N 128.600 0.3 1 34 37 37 GLY C C 171.180 0.3 1 35 37 37 GLY CA C 45.078 0.3 1 36 37 37 GLY N N 114.660 0.3 1 37 38 38 LEU C C 174.072 0.3 1 38 38 38 LEU CA C 53.930 0.3 1 39 38 38 LEU CB C 44.264 0.3 1 40 38 38 LEU N N 133.718 0.3 1 41 39 39 THR C C 174.243 0.3 1 42 39 39 THR CA C 60.794 0.3 1 43 39 39 THR CB C 68.838 0.3 1 44 39 39 THR N N 124.170 0.3 1 45 40 40 GLU C C 176.430 0.3 1 46 40 40 GLU CA C 57.224 0.3 1 47 40 40 GLU CB C 30.758 0.3 1 48 40 40 GLU N N 125.270 0.3 1 49 45 45 PHE CA C 57.306 0.3 1 50 45 45 PHE CB C 42.717 0.3 1 51 45 45 PHE N N 126.173 0.3 1 52 50 50 ALA C C 176.247 0.3 1 53 50 50 ALA CA C 53.468 0.3 1 54 50 50 ALA N N 128.458 0.3 1 55 51 51 GLY C C 171.603 0.3 1 56 51 51 GLY CA C 48.585 0.3 1 57 51 51 GLY N N 113.646 0.3 1 58 52 52 GLY C C 173.102 0.3 1 59 52 52 GLY CA C 46.894 0.3 1 60 52 52 GLY N N 115.100 0.3 1 61 58 58 THR C C 172.107 0.3 1 62 58 58 THR CA C 60.882 0.3 1 63 58 58 THR CB C 71.437 0.3 1 64 58 58 THR N N 122.404 0.3 1 65 59 59 ALA C C 174.615 0.3 1 66 59 59 ALA CA C 49.948 0.3 1 67 59 59 ALA CB C 21.477 0.3 1 68 59 59 ALA N N 129.563 0.3 1 69 62 62 ASP C C 174.490 0.3 1 70 62 62 ASP CA C 57.024 0.3 1 71 62 62 ASP CB C 39.853 0.3 1 72 63 63 GLY C C 171.036 0.3 1 73 63 63 GLY CA C 44.721 0.3 1 74 63 63 GLY N N 110.047 0.3 1 75 64 64 VAL C C 173.289 0.3 1 76 64 64 VAL CA C 60.722 0.3 1 77 64 64 VAL CB C 35.315 0.3 1 78 64 64 VAL N N 122.790 0.3 1 79 65 65 ALA CB C 22.130 0.3 1 80 65 65 ALA N N 127.997 0.3 1 81 77 77 SER C C 171.254 0.3 1 82 77 77 SER CA C 55.407 0.3 1 83 77 77 SER CB C 63.407 0.3 1 84 77 77 SER N N 125.500 0.3 1 85 78 78 GLY C C 171.303 0.3 1 86 78 78 GLY CA C 44.034 0.3 1 87 78 78 GLY N N 116.309 0.3 1 88 79 79 ASP C C 176.113 0.3 1 89 79 79 ASP CA C 51.223 0.3 1 90 79 79 ASP CB C 41.896 0.3 1 91 79 79 ASP N N 119.442 0.3 1 92 80 80 HIS C C 174.830 0.3 1 93 80 80 HIS CA C 56.729 0.3 1 94 80 80 HIS CB C 25.359 0.3 1 95 80 80 HIS N N 110.906 0.3 1 96 81 81 SER C C 173.140 0.3 1 97 81 81 SER CA C 57.928 0.3 1 98 81 81 SER CB C 67.415 0.3 1 99 81 81 SER N N 118.278 0.3 1 100 82 82 ILE C C 175.454 0.3 1 101 82 82 ILE CA C 60.671 0.3 1 102 82 82 ILE CB C 36.393 0.3 1 103 82 82 ILE N N 121.532 0.3 1 104 83 83 ILE C C 174.407 0.3 1 105 83 83 ILE CA C 61.147 0.3 1 106 83 83 ILE CB C 36.487 0.3 1 107 83 83 ILE N N 124.051 0.3 1 stop_ save_