data_25558 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; MAX1 peptide fibril ; _BMRB_accession_number 25558 _BMRB_flat_file_name bmr25558.str _Entry_type original _Submission_date 2015-03-30 _Accession_date 2015-03-30 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Structure of 20-residue MAX1 peptide fibril in hydrogels' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nagy-Smith Katelyn . . 2 Moore Eric . . 3 Schneider Joel . . 4 Tycko Robert . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 37 "15N chemical shifts" 4 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-07-27 original BMRB . stop_ _Original_release_date 2015-07-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Molecular-level Architecture of Self-Assembled Peptide Fibrils from Solid State NMR ; _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 Nagy-Smith Katelyn . . 2 Moore Eric . . 3 Schneider Joel . . 4 Tycko Robert . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _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 'MAX1 peptide fibril' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $MAX1 entity_2 $MAX1 entity_3 $MAX1 entity_4 $MAX1 entity_5 $MAX1 entity_6 $MAX1 entity_7 $MAX1 entity_8 $MAX1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_MAX1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common MAX1 _Molecular_mass 2238.995 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; VKVKVKVKVXPTKVKVKVKV X ; loop_ _Residue_seq_code _Residue_label 1 VAL 2 LYS 3 VAL 4 LYS 5 VAL 6 LYS 7 VAL 8 LYS 9 VAL 10 DPR 11 PRO 12 THR 13 LYS 14 VAL 15 LYS 16 VAL 17 LYS 18 VAL 19 LYS 20 VAL 21 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DPR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-PROLINE _BMRB_code DPR _PDB_code DPR _Standard_residue_derivative . _Molecular_mass 115.130 _Mol_paramagnetic . _Details . 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 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 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 . ? 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 CD ? ? SING N H ? ? 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 HD2 ? ? SING CD HD3 ? ? 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 _Details $MAX1 . . . . . . 'Designed, synthetic peptide.' 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 $MAX1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-V1; 15N-V20]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-V3; 15N-V18]' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-V5; 15N-V16]' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-V7; 15N-V14]' stop_ save_ save_sample_5 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-V1; 13CO-V16]' stop_ save_ save_sample_6 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-V3; 13CO-V16]' stop_ save_ save_sample_7 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-V5; 13CO-V16]' stop_ save_ save_sample_8 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-V7; 13CO-V16]' stop_ save_ save_sample_9 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[13CO-P10; U-15N,13C-(K8, V9, )11, T12, K13]' stop_ save_ save_sample_10 _Saveframe_category sample _Sample_type 'fibrillar hydrogel' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MAX1 . mM '[U-15N,13C-(V1, P11, T12, V20)]' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'stage 1 of structure development' stop_ _Details . save_ save_NAMD _Saveframe_category software _Name NAMD _Version . loop_ _Vendor _Address _Electronic_address 'Klaus Schulten and coworkers' . . stop_ loop_ _Task 'stage 2 of structure development' stop_ _Details ; Hybrid Monte Carlo/Molecular Dynamics calculation, using NAMD to generate moves and NMR-based potentials to determine acceptance. Performed in explicit solvent. ; save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model InfinityPlus _Field_strength 400 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III' _Field_strength 400 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Infinity _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_REDOR_1 _Saveframe_category NMR_applied_experiment _Experiment_name REDOR _Sample_label $sample_1 save_ save_REDOR_2 _Saveframe_category NMR_applied_experiment _Experiment_name REDOR _Sample_label $sample_2 save_ save_REDOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name REDOR _Sample_label $sample_3 save_ save_REDOR_4 _Saveframe_category NMR_applied_experiment _Experiment_name REDOR _Sample_label $sample_4 save_ save_PITHIRDS-CT_5 _Saveframe_category NMR_applied_experiment _Experiment_name PITHIRDS-CT _Sample_label $sample_1 save_ save_PITHIRDS-CT_6 _Saveframe_category NMR_applied_experiment _Experiment_name PITHIRDS-CT _Sample_label $sample_2 save_ save_PITHIRDS-CT_7 _Saveframe_category NMR_applied_experiment _Experiment_name PITHIRDS-CT _Sample_label $sample_3 save_ save_PITHIRDS-CT_8 _Saveframe_category NMR_applied_experiment _Experiment_name PITHIRDS-CT _Sample_label $sample_4 save_ save_PITHIRDS-CT_9 _Saveframe_category NMR_applied_experiment _Experiment_name PITHIRDS-CT _Sample_label $sample_5 save_ save_PITHIRDS-CT_10 _Saveframe_category NMR_applied_experiment _Experiment_name PITHIRDS-CT _Sample_label $sample_6 save_ save_PITHIRDS-CT_11 _Saveframe_category NMR_applied_experiment _Experiment_name PITHIRDS-CT _Sample_label $sample_7 save_ save_PITHIRDS-CT_12 _Saveframe_category NMR_applied_experiment _Experiment_name PITHIRDS-CT _Sample_label $sample_8 save_ save_15N-BARE_13 _Saveframe_category NMR_applied_experiment _Experiment_name 15N-BARE _Sample_label $sample_9 save_ save_13C-BARE_14 _Saveframe_category NMR_applied_experiment _Experiment_name 13C-BARE _Sample_label $sample_9 save_ save_2D_RAD/DARR_15 _Saveframe_category NMR_applied_experiment _Experiment_name '2D RAD/DARR' _Sample_label $sample_10 save_ save_2D_NCACX_16 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NCACX' _Sample_label $sample_10 save_ save_2D_RAD/DARR_17 _Saveframe_category NMR_applied_experiment _Experiment_name '2D RAD/DARR' _Sample_label $sample_9 save_ save_2D_NCACX_18 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NCACX' _Sample_label $sample_9 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' 0 . M pH 9 . pH pressure 1 . atm temperature 273 . 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 powder' C 13 carboxylate ppm 179.65 external direct . . . 1.0 'liquid anhydrous ammonia' N 15 nitrogen ppm 0.0 external indirect . . . 0.402907564 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 RAD/DARR' '2D NCACX' stop_ loop_ _Sample_label $sample_10 $sample_9 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name entity_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 VAL C C 177.1 0.2 1 2 1 1 VAL CA C 63.1 0.2 1 3 1 1 VAL CB C 36.3 0.2 1 4 1 1 VAL CG1 C 21.6 0.2 2 5 1 1 VAL CG2 C 21.6 0.2 2 6 8 8 LYS C C 174.2 0.2 1 7 8 8 LYS CA C 54.4 0.2 1 8 8 8 LYS CB C 36.0 0.2 1 9 8 8 LYS CG C 25.1 0.2 1 10 8 8 LYS CD C 29.7 0.2 1 11 8 8 LYS CE C 42.4 0.2 1 12 8 8 LYS N N 125.3 0.2 1 13 9 9 VAL C C 172.4 0.2 1 14 9 9 VAL CA C 58.1 0.2 1 15 9 9 VAL CB C 32.9 0.2 1 16 9 9 VAL CG1 C 20.9 0.2 2 17 9 9 VAL CG2 C 20.9 0.2 2 18 10 10 DPR C C 174.9 0.2 1 19 11 11 PRO C C 175.9 0.2 1 20 11 11 PRO CA C 63.1 0.2 1 21 11 11 PRO CB C 32.1 0.2 1 22 11 11 PRO CG C 25.9 0.2 1 23 11 11 PRO CD C 49.9 0.2 1 24 11 11 PRO N N 132.9 0.2 1 25 12 12 THR C C 172.5 0.2 1 26 12 12 THR CA C 63.1 0.2 1 27 12 12 THR CB C 68.9 0.2 1 28 12 12 THR CG2 C 21.6 0.2 1 29 12 12 THR N N 118.1 0.2 1 30 13 13 LYS C C 174.2 0.2 1 31 13 13 LYS CA C 54.4 0.2 1 32 13 13 LYS CB C 36.0 0.2 1 33 13 13 LYS CG C 25.1 0.2 1 34 13 13 LYS CD C 29.7 0.2 1 35 13 13 LYS CE C 42.4 0.2 1 36 20 20 VAL C C 177.5 0.2 1 37 20 20 VAL CA C 60.3 0.2 1 38 20 20 VAL CB C 33.0 0.2 1 39 20 20 VAL CG1 C 20.9 0.2 2 40 20 20 VAL CG2 C 20.9 0.2 2 41 20 20 VAL N N 123.8 0.2 1 stop_ save_