data_5735 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Solution Structure of Rat Ab-(1-28) and its Interaction with Zinc: Insights into the Scarity of Amyloid Deposition in Aged Rat Brain ; _BMRB_accession_number 5735 _BMRB_flat_file_name bmr5735.str _Entry_type original _Submission_date 2003-03-13 _Accession_date 2003-03-14 _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 Huang J. . . 2 Yao Y. . . 3 Tang W. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 158 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2004-10-18 original author . stop_ _Original_release_date 2004-10-18 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The Solution Structure of Rat Abeta-(1-28) and its Interaction with Zinc ion: Insights into the Scarity of Amyloid Deposition in Aged Rat Brain ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15160315 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huang J. . . 2 Yao Y. . . 3 Lin J. . . 4 Ye Y. H. . 5 Sun W. Y. . 6 Tang W. . . stop_ _Journal_abbreviation 'J. Biol. Inorg. Chem.' _Journal_volume 9 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 627 _Page_last 635 _Year 2004 _Details . loop_ _Keyword Glycoprotein Amyloid stop_ save_ ################################## # Molecular system description # ################################## save_system_rat_amyloid_beta-peptide_1-28 _Saveframe_category molecular_system _Mol_system_name 'rat amyloid beta-peptide 1-28' _Abbreviation_common 'rat amyloid beta-peptide 1-28' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'rat amyloid beta-peptide (1-28)' $Ab_(1-28) stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Ab_(1-28) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'rat amyloid beta-peptide (1-28)' _Abbreviation_common 'Ab (1-28)' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; DAEFGHDSGFEVRHQKLVFF AEDVGSNK ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 ALA 3 GLU 4 PHE 5 GLY 6 HIS 7 ASP 8 SER 9 GLY 10 PHE 11 GLU 12 VAL 13 ARG 14 HIS 15 GLN 16 LYS 17 LEU 18 VAL 19 PHE 20 PHE 21 ALA 22 GLU 23 ASP 24 VAL 25 GLY 26 SER 27 ASN 28 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 17884 rat_beta_amyloid 57.14 18 100.00 100.00 1.77e-01 PDB 1NMJ "The Solution Structure Of Rat Ab-(1-28) And Its Interaction With Zinc: Insights Into The Scarity Of Amyloid Deposition In Aged " 92.86 28 100.00 100.00 1.58e-08 PDB 2LI9 "Metal Binding Domain Of Rat Beta-Amyloid" 57.14 18 100.00 100.00 1.77e-01 DBJ BAC34997 "unnamed protein product [Mus musculus]" 100.00 218 100.00 100.00 2.66e-10 DBJ BAC36369 "unnamed protein product [Mus musculus]" 100.00 384 100.00 100.00 9.49e-10 DBJ BAE27986 "unnamed protein product [Mus musculus]" 100.00 695 100.00 100.00 2.17e-09 DBJ BAE34927 "unnamed protein product [Mus musculus]" 100.00 752 100.00 100.00 1.33e-09 DBJ BAE35313 "unnamed protein product [Mus musculus]" 100.00 752 100.00 100.00 1.72e-09 EMBL CAA30488 "unnamed protein product [Rattus rattus]" 100.00 695 100.00 100.00 1.99e-09 GB AAA37139 "beta-amyloid protein [Mus musculus]" 100.00 695 100.00 100.00 2.07e-09 GB AAB40919 "amyloid precursor protein [Mus musculus]" 100.00 82 100.00 100.00 9.27e-11 GB AAB41502 "hippocampal amyloid precursor protein [Mus musculus]" 100.00 695 100.00 100.00 2.17e-09 GB AAB86608 "Alzheimer's amyloid beta protein precursor [Cricetulus griseus]" 100.00 79 100.00 100.00 6.88e-11 GB AAH05490 "App protein, partial [Mus musculus]" 100.00 607 100.00 100.00 7.03e-09 REF NP_001185752 "amyloid beta A4 protein isoform 1 precursor [Mus musculus]" 100.00 770 100.00 100.00 1.39e-09 REF NP_001185753 "amyloid beta A4 protein isoform 3 precursor [Mus musculus]" 100.00 751 100.00 100.00 1.85e-09 REF NP_001185754 "amyloid beta A4 protein isoform 5 precursor [Mus musculus]" 100.00 733 100.00 100.00 2.26e-09 REF NP_001185755 "amyloid beta A4 protein isoform 6 precursor [Mus musculus]" 100.00 752 100.00 100.00 1.72e-09 REF NP_031497 "amyloid beta A4 protein isoform 2 precursor [Mus musculus]" 100.00 695 100.00 100.00 2.17e-09 SP P08592 "RecName: Full=Amyloid beta A4 protein; AltName: Full=ABPP; Short=APP; AltName: Full=Alzheimer disease amyloid A4 protein homolo" 100.00 770 100.00 100.00 1.39e-09 SP P12023 "RecName: Full=Amyloid beta A4 protein; AltName: Full=ABPP; Short=APP; AltName: Full=Alzheimer disease amyloid A4 protein homolo" 100.00 770 100.00 100.00 1.39e-09 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Organ $Ab_(1-28) Rat 10116 Eukaryota Metazoa Rattus norvegicus brain 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 $Ab_(1-28) vendor . . . . . 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 _Concentration_min_value _Isotopic_labeling $Ab_(1-28) 2 mM . . DMSO . mM 2.0 . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_DQF-COSY_2 _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 pD 6.8 0.3 n/a temperature 298 0.5 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 _Indirect_shift_ratio _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 $entry_citation $entry_citation 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 'rat amyloid beta-peptide (1-28)' _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 ASP HB3 H 2.66 . . 2 . 1 ASP HB2 H 2.84 . . 3 . 1 ASP HA H 4.1 . . 4 . 2 ALA H H 8.59 . . 5 . 2 ALA HA H 4.32 . . 6 . 2 ALA HB H 1.18 . . 7 . 3 GLU H H 8.05 . . 8 . 3 GLU HB3 H 1.67 . . 9 . 3 GLU HG2 H 2.17 . . 10 . 3 GLU HA H 4.2 . . 11 . 3 GLU HB2 H 1.83 . . 12 . 4 PHE H H 7.94 . . 13 . 4 PHE HB3 H 2.79 . . 14 . 4 PHE HD1 H 7.23 . . 15 . 4 PHE HD2 H 7.23 . . 16 . 4 PHE HA H 4.52 . . 17 . 4 PHE HB2 H 3.02 . . 18 . 5 GLY H H 8.32 . . 19 . 5 GLY HA2 H 3.78 . . 20 . 5 GLY HA3 H 3.72 . . 21 . 6 HIS H H 8.18 . . 22 . 6 HIS HB3 H 2.96 . . 23 . 6 HIS HD2 H 8.95 . . 24 . 6 HIS HE1 H 7.35 . . 25 . 6 HIS HA H 4.62 . . 26 . 6 HIS HB2 H 3.08 . . 27 . 7 ASP H H 8.43 . . 28 . 7 ASP HB3 H 2.52 . . 29 . 7 ASP HA H 4.63 . . 30 . 7 ASP HB2 H 2.78 . . 31 . 8 SER H H 8 . . 32 . 8 SER HB3 H 3.54 . . 33 . 8 SER HA H 4.24 . . 34 . 8 SER HB2 H 3.61 . . 35 . 9 GLY H H 8.04 . . 36 . 9 GLY HA2 H 3.72 . . 37 . 9 GLY HA3 H 3.63 . . 38 . 10 PHE H H 8.04 . . 39 . 10 PHE HB3 H 2.72 . . 40 . 10 PHE HD1 H 7.22 . . 41 . 10 PHE HD2 H 7.22 . . 42 . 10 PHE HA H 4.55 . . 43 . 10 PHE HB2 H 2.99 . . 44 . 11 GLU H H 8.27 . . 45 . 11 GLU HB3 H 1.72 . . 46 . 11 GLU HG2 H 2.26 . . 47 . 11 GLU HG3 H 2.26 . . 48 . 11 GLU HA H 4.33 . . 49 . 11 GLU HB2 H 1.89 . . 50 . 12 VAL H H 7.72 . . 51 . 12 VAL HG1 H 0.81 . . 52 . 12 VAL HG2 H 0.81 . . 53 . 12 VAL HA H 4.19 . . 54 . 12 VAL HB H 1.93 . . 55 . 13 ARG H H 8.17 . . 56 . 13 ARG HB3 H 1.51 . . 57 . 13 ARG HG2 H 1.43 . . 58 . 13 ARG HG3 H 1.43 . . 59 . 13 ARG HD2 H 3.08 . . 60 . 13 ARG HD3 H 3.08 . . 61 . 13 ARG HE H 7.55 . . 62 . 13 ARG HA H 4.23 . . 63 . 13 ARG HB2 H 1.63 . . 64 . 14 HIS H H 8.23 . . 65 . 14 HIS HB3 H 2.94 . . 66 . 14 HIS HD2 H 8.95 . . 67 . 14 HIS HE1 H 7.35 . . 68 . 14 HIS HA H 4.6 . . 69 . 14 HIS HB2 H 3.05 . . 70 . 15 GLN H H 8.11 . . 71 . 15 GLN HB3 H 1.74 . . 72 . 15 GLN HG2 H 2.10 . . 73 . 15 GLN HG3 H 2.10 . . 74 . 15 GLN HE21 H 7.30 . . 75 . 15 GLN HE22 H 6.87 . . 76 . 15 GLN HA H 4.23 . . 77 . 15 GLN HB2 H 1.86 . . 78 . 16 LYS H H 8.23 . . 79 . 16 LYS HB3 H 1.61 . . 80 . 16 LYS HG2 H 1.28 . . 81 . 16 LYS HG3 H 1.28 . . 82 . 16 LYS HD2 H 1.49 . . 83 . 16 LYS HD3 H 1.49 . . 84 . 16 LYS HE2 H 2.71 . . 85 . 16 LYS HE3 H 2.71 . . 86 . 16 LYS HZ H 7.77 . . 87 . 16 LYS HA H 4.24 . . 88 . 16 LYS HB2 H 1.61 . . 89 . 17 LEU H H 7.99 . . 90 . 17 LEU HB3 H 1.42 . . 91 . 17 LEU HD1 H 0.84 . . 92 . 17 LEU HD2 H 0.78 . . 93 . 17 LEU HG H 1.54 . . 94 . 17 LEU HA H 4.32 . . 95 . 17 LEU HB2 H 1.34 . . 96 . 18 VAL H H 7.73 . . 97 . 18 VAL HG1 H 0.70 . . 98 . 18 VAL HG2 H 0.70 . . 99 . 18 VAL HA H 4.08 . . 100 . 18 VAL HB H 1.84 . . 101 . 19 PHE H H 7.92 . . 102 . 19 PHE HB3 H 2.72 . . 103 . 19 PHE HD1 H 7.18 . . 104 . 19 PHE HD2 H 7.18 . . 105 . 19 PHE HE1 H 7.23 . . 106 . 19 PHE HE2 H 7.23 . . 107 . 19 PHE HA H 4.52 . . 108 . 19 PHE HB2 H 2.94 . . 109 . 20 PHE H H 8.1 . . 110 . 20 PHE HB3 H 2.81 . . 111 . 20 PHE HD1 H 7.23 . . 112 . 20 PHE HD2 H 7.23 . . 113 . 20 PHE HE1 H 7.16 . . 114 . 20 PHE HE2 H 7.16 . . 115 . 20 PHE HA H 4.56 . . 116 . 20 PHE HB2 H 3.02 . . 117 . 21 ALA H H 8.18 . . 118 . 21 ALA HA H 4.31 . . 119 . 21 ALA HB H 1.21 . . 120 . 22 GLU H H 8.02 . . 121 . 22 GLU HB3 H 1.74 . . 122 . 22 GLU HG2 H 2.25 . . 123 . 22 GLU HG3 H 2.25 . . 124 . 22 GLU HA H 4.3 . . 125 . 22 GLU HB2 H 1.89 . . 126 . 23 ASP H H 8.27 . . 127 . 23 ASP HB3 H 2.72 . . 128 . 23 ASP HA H 4.6 . . 129 . 23 ASP HB2 H 2.52 . . 130 . 24 VAL H H 7.66 . . 131 . 24 VAL HG1 H 0.85 . . 132 . 24 VAL HG2 H 0.81 . . 133 . 24 VAL HA H 4.15 . . 134 . 24 VAL HB H 1.98 . . 135 . 25 GLY H H 8.15 . . 136 . 25 GLY HA2 H 3.81 . . 137 . 25 GLY HA3 H 3.72 . . 138 . 26 SER H H 7.95 . . 139 . 26 SER HB3 H 3.52 . . 140 . 26 SER HA H 4.33 . . 141 . 26 SER HB2 H 3.59 . . 142 . 27 ASN H H 8.23 . . 143 . 27 ASN HB3 H 2.46 . . 144 . 27 ASN HD21 H 7.37 . . 145 . 27 ASN HD22 H 6.93 . . 146 . 27 ASN HA H 4.6 . . 147 . 27 ASN HB2 H 2.55 . . 148 . 28 LYS H H 7.92 . . 149 . 28 LYS HB3 H 1.58 . . 150 . 28 LYS HG2 H 1.33 . . 151 . 28 LYS HG3 H 1.33 . . 152 . 28 LYS HD2 H 1.51 . . 153 . 28 LYS HD3 H 1.51 . . 154 . 28 LYS HE2 H 2.76 . . 155 . 28 LYS HE3 H 2.76 . . 156 . 28 LYS HZ H 7.70 . . 157 . 28 LYS HA H 4.14 . . 158 . 28 LYS HB2 H 1.71 . . stop_ save_