data_30227 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Zinc-Binding Structure of a Catalytic Amyloid from Solid-State NMR Spectroscopy ; _BMRB_accession_number 30227 _BMRB_flat_file_name bmr30227.str _Entry_type original _Submission_date 2017-01-09 _Accession_date 2017-01-09 _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 Lee M. . . 2 Wang T. . . 3 Makhlynets O. V. . 4 Wu Y. . . 5 Polizzi N. . . 6 Wu H. . . 7 Gosavi P. M. . 8 Korendovych I. V. . 9 DeGrado W. F. . 10 Hong M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 69 "15N chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-05-25 original BMRB . stop_ _Original_release_date 2017-02-02 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Zinc-Binding Structure of a Catalytic Amyloid from Solid-State NMR Spectroscopy ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee M. . . 2 Wang T. . . 3 Makhlynets O. V. . 4 Wu Y. . . 5 Polizzi N. . . 6 Wu H. . . 7 Gosavi P. M. . 8 Korendovych I. V. . 9 DeGrado W. F. . 10 Hong M. . . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name ILE-HIS-VAL-HIS-LEU-GLN-ILE _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 'entity_1, 3' $entity_1 'entity_1, 4' $entity_1 'entity_1, 5' $entity_1 'entity_1, 6' $entity_1 'entity_1, 7' $entity_1 'entity_1, 8' $entity_1 'entity_1, 9' $entity_1 'entity_1, 10' $entity_1 'entity_1, 11' $entity_1 'entity_1, 12' $entity_1 'entity_ZN, 1' $entity_ZN 'entity_ZN, 2' $entity_ZN 'entity_ZN, 3' $entity_ZN 'entity_ZN, 4' $entity_ZN 'entity_ZN, 5' $entity_ZN 'entity_ZN, 6' $entity_ZN 'entity_ZN, 7' $entity_ZN 'entity_ZN, 8' $entity_ZN 'entity_ZN, 9' $entity_ZN 'entity_ZN, 10' $entity_ZN 'entity_ZN, 11' $entity_ZN 'entity_ZN, 12' $entity_ZN stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 861.042 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ; IHVHLQI ; loop_ _Residue_seq_code _Residue_label 1 ILE 2 HIS 3 VAL 4 HIS 5 LEU 6 GLN 7 ILE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_ZN (ZINC ION)" _BMRB_code ZN _PDB_code ZN _Molecular_mass 65.409 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons ZN ZN ZN . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 . 32630 . . . . 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solid _Details '0.4 g/L [U-13C; U-15N] IVL, pH 8 Tris buffer' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 g/L '[U-13C; U-15N]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solid _Details '0.4 g/L [U-13C] mixed sample, pH 8 Tris buffer' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 g/L [U-13C] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Bruker _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_correlation_spectra_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C correlation spectra' _Sample_label $sample_1 save_ save_2D_15N-13C_correlation_spectra_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C correlation spectra' _Sample_label $sample_1 save_ save_REDOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name REDOR _Sample_label $sample_1 save_ save_2D_13C-13C_correlation_spectra_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C correlation spectra' _Sample_label $sample_2 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' 100 . mM pH 8 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 adamantane C 13 'methylene protons' ppm 38.48 external indirect . . . 0.251449519 N-formyl-Met-Leu-Phe-OH N 15 nitrogen ppm 127.88 external indirect . . . 0.101329112 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_chemical_shifts_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 13C-13C correlation spectra' '2D 15N-13C correlation spectra' REDOR stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 ILE C C 171.80 0.20 . 2 1 1 ILE CA C 58.80 0.20 . 3 1 1 ILE CB C 39.90 0.20 . 4 1 1 ILE CG1 C 25.00 0.20 . 5 1 1 ILE CG2 C 15.70 0.20 . 6 1 1 ILE CD1 C 12.90 0.20 . 7 1 1 ILE N N 125.00 0.20 . 8 2 2 HIS C C 171.50 0.20 . 9 2 2 HIS CA C 51.30 0.20 . 10 2 2 HIS CB C 31.80 0.20 . 11 2 2 HIS CG C 135.00 0.20 . 12 2 2 HIS CD2 C 121.90 0.20 . 13 2 2 HIS CE1 C 143.90 0.20 . 14 2 2 HIS N N 130.60 0.20 . 15 2 2 HIS ND1 N 210.50 0.20 . 16 2 2 HIS NE2 N 208.00 0.20 . 17 3 3 VAL C C 170.50 0.20 . 18 3 3 VAL CA C 58.50 0.20 . 19 3 3 VAL CB C 31.40 0.20 . 20 3 3 VAL CG1 C 18.60 0.20 2 21 3 3 VAL CG2 C 18.60 0.20 2 22 3 3 VAL N N 128.30 0.20 . 23 4 4 HIS C C 171.90 0.20 . 24 4 4 HIS CA C 50.50 0.20 . 25 4 4 HIS CB C 31.50 0.20 . 26 4 4 HIS CG C 135.70 0.20 . 27 4 4 HIS CD2 C 120.30 0.20 . 28 4 4 HIS CE1 C 144.50 0.20 . 29 4 4 HIS N N 129.30 0.20 . 30 4 4 HIS ND1 N 210.00 0.20 . 31 4 4 HIS NE2 N 207.00 0.20 . 32 5 5 LEU C C 172.80 0.20 . 33 5 5 LEU CA C 51.20 0.20 . 34 5 5 LEU CB C 43.50 0.20 . 35 5 5 LEU CG C 25.60 0.20 . 36 5 5 LEU CD1 C 24.50 0.20 2 37 5 5 LEU CD2 C 23.70 0.20 2 38 5 5 LEU N N 123.90 0.20 . 39 7 7 ILE C C 174.50 0.20 . 40 7 7 ILE CA C 57.60 0.20 . 41 7 7 ILE CB C 36.90 0.20 . 42 7 7 ILE CG1 C 25.30 0.20 . 43 7 7 ILE CG2 C 16.10 0.20 . 44 7 7 ILE CD1 C 11.70 0.20 . stop_ save_ save_assigned_chemical_shifts_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 13C-13C correlation spectra' '2D 15N-13C correlation spectra' REDOR stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 2' _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 ILE C C 171.80 0.20 . 2 1 1 ILE CA C 58.80 0.20 . 3 1 1 ILE CB C 39.30 0.20 . 4 1 1 ILE CG1 C 25.00 0.20 . 5 1 1 ILE CG2 C 15.70 0.20 . 6 1 1 ILE CD1 C 12.90 0.20 . 7 1 1 ILE N N 125.00 0.20 . 8 2 2 HIS C C 171.90 0.20 . 9 2 2 HIS CA C 52.80 0.20 . 10 2 2 HIS CB C 31.30 0.20 . 11 2 2 HIS CG C 135.50 0.20 . 12 2 2 HIS CD2 C 116.60 0.20 . 13 2 2 HIS CE1 C 139.10 0.20 . 14 2 2 HIS N N 128.20 0.20 . 15 2 2 HIS ND1 N 210.50 0.20 . 16 2 2 HIS NE2 N 174.50 0.20 . 17 3 3 VAL C C 170.50 0.20 . 18 3 3 VAL CA C 58.50 0.20 . 19 3 3 VAL CB C 31.40 0.20 . 20 3 3 VAL CG1 C 18.60 0.20 2 21 3 3 VAL CG2 C 18.60 0.20 2 22 3 3 VAL N N 128.30 0.20 . 23 4 4 HIS C C 171.90 0.20 . 24 4 4 HIS CA C 52.80 0.20 . 25 4 4 HIS CB C 31.60 0.20 . 26 4 4 HIS CG C 135.20 0.20 . 27 4 4 HIS CD2 C 116.80 0.20 . 28 4 4 HIS CE1 C 138.70 0.20 . 29 4 4 HIS N N 130.40 0.20 . 30 4 4 HIS ND1 N 210.00 0.20 . 31 4 4 HIS NE2 N 207.00 0.20 . 32 5 5 LEU C C 171.60 0.20 . 33 5 5 LEU CA C 51.20 0.20 . 34 5 5 LEU CB C 43.50 0.20 . 35 5 5 LEU CG C 25.60 0.20 . 36 5 5 LEU CD1 C 24.50 0.20 2 37 5 5 LEU CD2 C 23.70 0.20 2 38 5 5 LEU N N 123.90 0.20 . 39 7 7 ILE C C 174.50 0.20 . 40 7 7 ILE CA C 57.60 0.20 . 41 7 7 ILE CB C 37.60 0.20 . 42 7 7 ILE CG1 C 25.30 0.20 . 43 7 7 ILE CG2 C 16.10 0.20 . stop_ save_