data_2KV5 # _entry.id 2KV5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2KV5 RCSB RCSB101611 WWPDB D_1000101611 # _pdbx_database_related.db_name BMRB _pdbx_database_related.db_id 16769 _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KV5 _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2010-03-08 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zangger, K.' 1 'Gobl, C.' 2 'Kosol, S.' 3 'Ruckert, H.M.' 4 # _citation.id primary _citation.title 'Solution structure and membrane binding of the toxin fst of the par addiction module' _citation.journal_abbrev Biochemistry _citation.journal_volume 49 _citation.page_first 6567 _citation.page_last 6575 _citation.year 2010 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20677831 _citation.pdbx_database_id_DOI 10.1021/bi1005128 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Gobl, C.' 1 primary 'Kosol, S.' 2 primary 'Stockner, T.' 3 primary 'Ruckert, H.M.' 4 primary 'Zangger, K.' 5 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Putative uncharacterized protein RNAI' _entity.formula_weight 3767.479 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name Fst # _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 MKDLMSLVIAPIFVGLVLEMISRVLDEEDDSRK _entity_poly.pdbx_seq_one_letter_code_can MKDLMSLVIAPIFVGLVLEMISRVLDEEDDSRK _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 MET n 1 2 LYS n 1 3 ASP n 1 4 LEU n 1 5 MET n 1 6 SER n 1 7 LEU n 1 8 VAL n 1 9 ILE n 1 10 ALA n 1 11 PRO n 1 12 ILE n 1 13 PHE n 1 14 VAL n 1 15 GLY n 1 16 LEU n 1 17 VAL n 1 18 LEU n 1 19 GLU n 1 20 MET n 1 21 ILE n 1 22 SER n 1 23 ARG n 1 24 VAL n 1 25 LEU n 1 26 ASP n 1 27 GLU n 1 28 GLU n 1 29 ASP n 1 30 ASP n 1 31 SER n 1 32 ARG n 1 33 LYS 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 'Enterococcus faecalis' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 1351 _pdbx_entity_src_syn.details 'synthesized by FMOC-based solid-phase peptide synthesis' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q9RLG7_ENTFA _struct_ref.pdbx_db_accession Q9RLG7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code MKDLMSLVIAPIFVGLVLEMISRVLDEEDDSRK _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2KV5 _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 33 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9RLG7 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 33 _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 33 # 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 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 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 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.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H TOCSY' 1 2 1 '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.15 _pdbx_nmr_exptl_sample_conditions.pH 5.0 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 303 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '50mM potassium phosphate; 100mM [U-99% 2H] DPC; 0.02% sodium azide; 90% H2O/10% D2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 600 Varian UNITY 1 'Varian Unity' 500 Bruker Avance 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2KV5 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KV5 _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.representative_conformer 1 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2KV5 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe ? 1 'Johnson, One Moon Scientific' 'data analysis' NMRView ? 2 ? refinement CNS 1.1 3 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KV5 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KV5 _struct.title 'Solution structure of the par toxin Fst in DPC micelles' _struct.pdbx_descriptor 'Putative uncharacterized protein RNAI' _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KV5 _struct_keywords.pdbx_keywords TOXIN _struct_keywords.text 'toxin-antitoxin, bacterial, toxin' # _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_biol.details ? # _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 LEU _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 4 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id LEU _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 LEU _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 4 _struct_conf.end_auth_comp_id LEU _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 22 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2KV5 _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 S # 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 MET 1 1 1 MET MET A . n A 1 2 LYS 2 2 2 LYS LYS A . n A 1 3 ASP 3 3 3 ASP ASP A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 MET 5 5 5 MET MET A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 LEU 7 7 7 LEU LEU A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 ILE 9 9 9 ILE ILE A . n A 1 10 ALA 10 10 10 ALA ALA A . n A 1 11 PRO 11 11 11 PRO PRO A . n A 1 12 ILE 12 12 12 ILE ILE A . n A 1 13 PHE 13 13 13 PHE PHE A . n A 1 14 VAL 14 14 14 VAL VAL A . n A 1 15 GLY 15 15 15 GLY GLY A . n A 1 16 LEU 16 16 16 LEU LEU A . n A 1 17 VAL 17 17 17 VAL VAL A . n A 1 18 LEU 18 18 18 LEU LEU A . n A 1 19 GLU 19 19 19 GLU GLU A . n A 1 20 MET 20 20 20 MET MET A . n A 1 21 ILE 21 21 21 ILE ILE A . n A 1 22 SER 22 22 22 SER SER A . n A 1 23 ARG 23 23 23 ARG ARG A . n A 1 24 VAL 24 24 24 VAL VAL A . n A 1 25 LEU 25 25 25 LEU LEU A . n A 1 26 ASP 26 26 26 ASP ASP A . n A 1 27 GLU 27 27 27 GLU GLU A . n A 1 28 GLU 28 28 28 GLU GLU A . n A 1 29 ASP 29 29 29 ASP ASP A . n A 1 30 ASP 30 30 30 ASP ASP A . n A 1 31 SER 31 31 31 SER SER A . n A 1 32 ARG 32 32 32 ARG ARG A . n A 1 33 LYS 33 33 33 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 2011-02-02 2 'Structure model' 1 1 2011-07-13 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id 'potassium phosphate-1' 50 ? mM ? 1 DPC-2 100 ? mM '[U-99% 2H]' 1 'sodium azide-3' 0.02 ? % ? 1 # 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 ASP A 3 ? ? -23.80 -50.39 2 1 PHE A 13 ? ? -66.64 -70.72 3 1 ASP A 26 ? ? -153.45 30.40 4 1 GLU A 28 ? ? -78.65 -75.03 5 1 SER A 31 ? ? -176.70 147.07 6 2 ASP A 3 ? ? -23.33 -49.54 7 2 VAL A 8 ? ? -95.40 -62.29 8 2 ASP A 26 ? ? -153.46 33.83 9 2 ASP A 29 ? ? 60.29 93.33 10 3 ASP A 3 ? ? -23.97 -50.37 11 3 VAL A 8 ? ? -94.72 -62.74 12 3 ASP A 26 ? ? -153.18 27.01 13 3 ARG A 32 ? ? 59.48 -173.30 14 4 ASP A 3 ? ? -24.25 -51.12 15 4 VAL A 8 ? ? -97.18 -64.11 16 4 ASP A 26 ? ? -153.40 33.49 17 4 SER A 31 ? ? 61.79 152.33 18 5 ASP A 3 ? ? -23.88 -51.50 19 5 VAL A 8 ? ? -94.73 -60.70 20 5 ASP A 26 ? ? -153.10 12.93 21 5 SER A 31 ? ? -174.47 36.95 22 6 ASP A 3 ? ? -23.83 -49.86 23 6 ASP A 26 ? ? -153.50 34.29 24 6 SER A 31 ? ? -144.36 -55.71 25 7 ASP A 3 ? ? -23.86 -50.89 26 7 ASP A 26 ? ? -153.29 22.27 27 7 GLU A 27 ? ? -66.47 92.57 28 7 GLU A 28 ? ? 63.53 141.28 29 7 ASP A 30 ? ? -168.76 80.17 30 8 ASP A 3 ? ? -23.94 -51.14 31 8 ASP A 26 ? ? -153.49 33.25 32 8 SER A 31 ? ? 60.73 106.51 33 9 ASP A 3 ? ? -24.68 -51.18 34 9 ASP A 26 ? ? -153.43 33.44 35 9 GLU A 28 ? ? -159.40 -45.56 36 10 ASP A 3 ? ? -24.18 -51.20 37 10 PHE A 13 ? ? -63.80 -70.58 38 10 ASP A 26 ? ? -153.49 32.85 39 10 ASP A 30 ? ? -98.34 35.76 40 11 ASP A 3 ? ? -24.04 -50.78 41 11 ILE A 9 ? ? -125.89 -54.38 42 11 ASP A 26 ? ? -153.47 34.13 43 11 GLU A 27 ? ? -66.81 -174.39 44 11 SER A 31 ? ? -65.11 98.35 45 12 ASP A 3 ? ? -24.28 -51.39 46 12 PHE A 13 ? ? -67.97 -70.12 47 12 ASP A 26 ? ? -153.35 32.92 48 12 GLU A 27 ? ? -69.06 70.22 49 12 GLU A 28 ? ? 60.01 83.54 50 12 SER A 31 ? ? -176.52 79.99 51 13 ASP A 3 ? ? -24.00 -50.18 52 13 VAL A 8 ? ? -95.21 -60.09 53 13 ASP A 26 ? ? -153.46 33.53 54 13 ASP A 30 ? ? -98.72 31.50 55 14 ASP A 3 ? ? -24.14 -51.34 56 14 VAL A 8 ? ? -97.03 -63.33 57 14 ASP A 26 ? ? -153.53 -50.54 58 14 GLU A 27 ? ? 41.51 83.14 59 14 ASP A 30 ? ? -141.65 -47.75 60 15 ASP A 3 ? ? -23.96 -51.20 61 15 PHE A 13 ? ? -61.42 -72.68 62 15 ASP A 26 ? ? -153.18 28.92 63 15 GLU A 27 ? ? -60.36 -173.95 64 15 ASP A 29 ? ? -91.29 51.00 65 15 ASP A 30 ? ? 60.70 107.01 66 16 ASP A 3 ? ? -24.02 -51.26 67 16 VAL A 8 ? ? -102.93 -62.72 68 16 PHE A 13 ? ? -66.44 -70.07 69 16 ASP A 26 ? ? -153.36 25.34 70 16 ASP A 30 ? ? 59.80 88.36 71 16 SER A 31 ? ? -60.08 -70.24 72 16 ARG A 32 ? ? 59.46 -178.59 73 17 ASP A 3 ? ? -24.12 -50.45 74 17 VAL A 8 ? ? -94.27 -62.80 75 17 PHE A 13 ? ? -65.06 -72.66 76 17 ASP A 26 ? ? -153.48 32.19 77 17 ASP A 30 ? ? -100.09 78.92 78 18 ASP A 3 ? ? -23.89 -50.96 79 18 PHE A 13 ? ? -61.94 -71.96 80 18 ASP A 26 ? ? -153.38 -38.62 81 18 GLU A 27 ? ? -47.96 166.51 82 19 ASP A 3 ? ? -24.01 -51.11 83 19 VAL A 8 ? ? -95.23 -61.36 84 19 ASP A 26 ? ? -153.46 33.08 85 20 ASP A 3 ? ? -23.84 -49.83 86 20 PHE A 13 ? ? -64.71 -72.19 87 20 ASP A 26 ? ? -153.50 32.44 88 20 GLU A 27 ? ? -98.89 31.63 89 20 ARG A 32 ? ? -143.17 -46.81 #