data_1RSX # _entry.id 1RSX # _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 1RSX pdb_00001rsx 10.2210/pdb1rsx/pdb RCSB RCSB021019 ? ? WWPDB D_1000021019 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1RSW _pdbx_database_related.details 'the same peptide complexed with Pb(II)' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1RSX _pdbx_database_status.recvd_initial_deposition_date 2003-12-10 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 'Ferrari, R.' 1 'Mendoza, G.' 2 'James, T.' 3 'Tonelli, M.' 4 'Basus, V.' 5 'Gasque, L.' 6 # _citation.id primary _citation.title 'Coordination Compounds derived from a dodecapeptide and Pb2+, Cd2+ and Zn2+. Modeling the site II from the Calbindin D9K' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ferrari, R.' 1 ? primary 'Mendoza, G.' 2 ? primary 'James, T.' 3 ? primary 'Tonelli, M.' 4 ? primary 'Basus, V.' 5 ? primary 'Gasque, L.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Vitamin D-dependent calcium-binding protein, intestinal' _entity.formula_weight 1326.301 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'residues 57-68 (SWS P02632)' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'CABP, Calbindin D9K' # _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 DKNGDGEVSFEE _entity_poly.pdbx_seq_one_letter_code_can DKNGDGEVSFEE _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 LYS n 1 3 ASN n 1 4 GLY n 1 5 ASP n 1 6 GLY n 1 7 GLU n 1 8 VAL n 1 9 SER n 1 10 PHE n 1 11 GLU n 1 12 GLU n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details ;Occurs naturaly in mammals calcium binding protein as the second calcium binding site. Purchased to Commonwealth Biotechnologies, Inc. as the trifluoroacetate salt, pur. min 95% ; # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code S100G_PIG _struct_ref.pdbx_db_accession P02632 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code DKNGDGEVSFEE _struct_ref.pdbx_align_begin 57 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1RSX _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P02632 _struct_ref_seq.db_align_beg 57 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 68 _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 12 # 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 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 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 noesyjr # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 288 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 6.6 _pdbx_nmr_exptl_sample_conditions.ionic_strength 'aprox 0' _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 '3mM Peptide and Cd(NO3)2. NaOH and HNO3 added for pH fixing to 6.6; 80% H2O, 20% D2O' _pdbx_nmr_sample_details.solvent_system '80% H2O, 20% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model UNITY _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1RSX _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1RSX _pdbx_nmr_ensemble.conformers_calculated_total_number 20 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'target function' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1RSX _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'fewest violations' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal NMRPipe 1.0 processing 'F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer, A. Bax' 1 MARDIGRAS 3.2 'iterative matrix relaxation' 'James, Borgias, Thomas, Liu, Kumar, Tonelli' 2 DYANA 1.5 'structure solution' 'Guenter, Mumenthaler, Herrmann' 3 DYANA 1.5 refinement 'Guenter, Mumenthaler, Herrmann' 4 # _exptl.entry_id 1RSX _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.density_Matthews ? # _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 1RSX _struct.title '12-mer from site II calbindin D9K (DKNGDGEVSFEE) coordinating Cd(II)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1RSX _struct_keywords.pdbx_keywords 'METAL BINDING PROTEIN' _struct_keywords.text 'EF-hand toxic metal ion transport model of ICaBP coordination toward cadmium, METAL BINDING 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 # _database_PDB_matrix.entry_id 1RSX _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 1RSX _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_ _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 LYS 2 2 2 LYS LYS A . n A 1 3 ASN 3 3 3 ASN ASN A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 ASP 5 5 5 ASP ASP A . n A 1 6 GLY 6 6 6 GLY GLY A . n A 1 7 GLU 7 7 7 GLU GLU A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 SER 9 9 9 SER SER 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 GLU 12 12 12 GLU GLU 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 2005-07-26 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _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_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 3 O A GLU 7 ? ? H A SER 9 ? ? 1.57 2 5 O A GLY 6 ? ? HG A SER 9 ? ? 1.45 3 6 H1 A ASP 1 ? ? OG A SER 9 ? ? 1.50 # 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 ASN A 3 ? ? -175.06 -39.41 2 1 GLU A 7 ? ? -44.07 160.34 3 1 SER A 9 ? ? -61.62 76.81 4 1 PHE A 10 ? ? 59.97 13.09 5 2 ASN A 3 ? ? 158.60 -54.60 6 2 ASP A 5 ? ? -147.39 32.60 7 2 GLU A 7 ? ? -33.77 149.79 8 2 VAL A 8 ? ? 30.97 48.45 9 2 SER A 9 ? ? -64.34 74.71 10 3 ASN A 3 ? ? 39.46 33.92 11 3 ASP A 5 ? ? 87.40 16.55 12 3 GLU A 7 ? ? -38.46 159.00 13 3 VAL A 8 ? ? -65.33 64.32 14 3 SER A 9 ? ? -62.65 74.56 15 3 PHE A 10 ? ? 56.31 15.02 16 4 ASN A 3 ? ? -167.59 -84.37 17 4 ASP A 5 ? ? 81.80 179.78 18 4 VAL A 8 ? ? 32.71 -149.46 19 4 SER A 9 ? ? 62.45 68.10 20 4 PHE A 10 ? ? 49.04 20.85 21 5 LYS A 2 ? ? -98.81 54.07 22 5 ASN A 3 ? ? 167.96 -35.73 23 5 ASP A 5 ? ? -124.35 -153.17 24 5 GLU A 7 ? ? -55.05 -177.37 25 5 VAL A 8 ? ? 35.00 47.37 26 6 LYS A 2 ? ? 28.67 62.01 27 6 ASN A 3 ? ? -164.22 -83.76 28 6 GLU A 7 ? ? -22.98 134.05 29 6 VAL A 8 ? ? 32.28 51.17 30 6 PHE A 10 ? ? 56.24 14.98 31 6 GLU A 11 ? ? -125.33 -169.87 32 7 ASN A 3 ? ? 93.92 14.46 33 7 ASP A 5 ? ? -63.99 -157.90 34 7 GLU A 7 ? ? -85.49 41.39 35 7 VAL A 8 ? ? -145.83 32.33 36 7 GLU A 11 ? ? -58.92 -169.99 37 8 ASN A 3 ? ? 173.42 -37.61 38 8 ASP A 5 ? ? 155.87 -176.33 39 8 GLU A 7 ? ? 51.06 172.60 40 8 VAL A 8 ? ? 35.10 36.49 41 8 GLU A 11 ? ? -66.82 -168.10 42 9 ASN A 3 ? ? -158.51 -67.26 43 9 ASP A 5 ? ? 39.35 30.92 44 9 VAL A 8 ? ? 31.17 51.19 45 9 GLU A 11 ? ? -53.42 -171.54 46 10 LYS A 2 ? ? -97.42 52.05 47 10 ASN A 3 ? ? -179.25 -69.41 48 10 VAL A 8 ? ? 37.73 30.80 49 10 GLU A 11 ? ? -50.71 -172.92 #