data_1NMJ # _entry.id 1NMJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1NMJ pdb_00001nmj 10.2210/pdb1nmj/pdb RCSB RCSB018005 ? ? WWPDB D_1000018005 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1AMB . unspecified PDB 1AMC . unspecified PDB 1BJB . unspecified PDB 1BJC . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NMJ _pdbx_database_status.recvd_initial_deposition_date 2003-01-10 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Huang, J.' 1 'Yao, Y.' 2 'Tang, W.X.' 3 # _citation.id primary _citation.title ;The solution structure of rat Abeta-(1-28) and its interaction with zinc ion: insights into the scarcity of amyloid deposition in aged rat brain ; _citation.journal_abbrev J.Biol.Inorg.Chem. _citation.journal_volume 9 _citation.page_first 627 _citation.page_last 635 _citation.year 2004 _citation.journal_id_ASTM JJBCFA _citation.country GW _citation.journal_id_ISSN 0949-8257 _citation.journal_id_CSD 2154 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15160315 _citation.pdbx_database_id_DOI 10.1007/s00775-004-0556-x # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Huang, J.' 1 ? primary 'Yao, Y.' 2 ? primary 'Lin, J.' 3 ? primary 'Ye, Y.H.' 4 ? primary 'Sun, W.Y.' 5 ? primary 'Tang, W.X.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description ;amyloid beta-peptide from Alzheimer's disease amyloid A4 protein homolog ; _entity.formula_weight 3171.411 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code DAEFGHDSGFEVRHQKLVFFAEDVGSNK _entity_poly.pdbx_seq_one_letter_code_can DAEFGHDSGFEVRHQKLVFFAEDVGSNK _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASP n 1 2 ALA n 1 3 GLU n 1 4 PHE n 1 5 GLY n 1 6 HIS n 1 7 ASP n 1 8 SER n 1 9 GLY n 1 10 PHE n 1 11 GLU n 1 12 VAL n 1 13 ARG n 1 14 HIS n 1 15 GLN n 1 16 LYS n 1 17 LEU n 1 18 VAL n 1 19 PHE n 1 20 PHE n 1 21 ALA n 1 22 GLU n 1 23 ASP n 1 24 VAL n 1 25 GLY n 1 26 SER n 1 27 ASN n 1 28 LYS n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name 'Norway rat' _entity_src_gen.gene_src_genus Rattus _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Rattus norvegicus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10116 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A4_RAT _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code DAEFGHDSGFEVRHQKLVFFAEDVGSNK _struct_ref.pdbx_align_begin 672 _struct_ref.pdbx_db_accession P08592 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1NMJ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 28 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P08592 _struct_ref_seq.db_align_beg 672 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 699 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 28 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D TOCSY' 2 1 1 '2D TOCSY' 3 1 1 DQF-COSY # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH ? _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '2mM rat ab-(1-28)' _pdbx_nmr_sample_details.solvent_system DMSO # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DRX _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_ensemble.entry_id 1NMJ _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? # _exptl.entry_id 1NMJ _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1NMJ _struct.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 ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NMJ _struct_keywords.pdbx_keywords 'MEMBRANE PROTEIN' _struct_keywords.text 'Glycoprotein, Amyloid, membrane protein' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id GLN _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 15 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id GLY _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 25 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id GLN _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 15 _struct_conf.end_auth_comp_id GLY _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 25 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 11 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 1NMJ _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1NMJ _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O # loop_ _database_PDB_caveat.text 'There are several chirality errors at the CA center.' # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ASP 1 1 1 ASP ASP A . n A 1 2 ALA 2 2 2 ALA ALA A . n A 1 3 GLU 3 3 3 GLU GLU A . n A 1 4 PHE 4 4 4 PHE PHE A . n A 1 5 GLY 5 5 5 GLY GLY A . n A 1 6 HIS 6 6 6 HIS HIS A . n A 1 7 ASP 7 7 7 ASP ASP A . n A 1 8 SER 8 8 8 SER SER A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 PHE 10 10 10 PHE PHE A . n A 1 11 GLU 11 11 11 GLU GLU A . n A 1 12 VAL 12 12 12 VAL VAL A . n A 1 13 ARG 13 13 13 ARG ARG A . n A 1 14 HIS 14 14 14 HIS HIS A . n A 1 15 GLN 15 15 15 GLN GLN A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 LEU 17 17 17 LEU LEU A . n A 1 18 VAL 18 18 18 VAL VAL A . n A 1 19 PHE 19 19 19 PHE PHE A . n A 1 20 PHE 20 20 20 PHE PHE A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 GLU 22 22 22 GLU GLU A . n A 1 23 ASP 23 23 23 ASP ASP A . n A 1 24 VAL 24 24 24 VAL VAL A . n A 1 25 GLY 25 25 25 GLY GLY A . n A 1 26 SER 26 26 26 SER SER A . n A 1 27 ASN 27 27 27 ASN ASN A . n A 1 28 LYS 28 28 28 LYS LYS A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2003-01-28 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU A 3 ? ? -72.57 46.03 2 1 PHE A 10 ? ? 1.33 -79.42 3 1 VAL A 12 ? ? 37.01 -75.42 4 1 ARG A 13 ? ? -70.51 33.17 5 1 HIS A 14 ? ? 54.72 12.07 6 1 GLN A 15 ? ? 58.60 -62.88 7 1 PHE A 19 ? ? -77.65 -82.56 8 1 ASN A 27 ? ? -0.73 -103.56 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 SER _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 26 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 ASN _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 27 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega 148.25 # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 CA ? A ASP 1 ? 'WRONG HAND' . 2 1 CA ? A ASN 27 ? 'WRONG HAND' . 3 1 CA ? A LYS 28 ? 'WRONG HAND' . #