data_7OB2 # _entry.id 7OB2 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 7OB2 pdb_00007ob2 10.2210/pdb7ob2/pdb WWPDB D_1292115390 ? ? BMRB 50902 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details . _pdbx_database_related.db_id 50902 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 7OB2 _pdbx_database_status.recvd_initial_deposition_date 2021-04-20 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Falcigno, L.' 1 0000-0002-3758-2716 ;D'Auria, G. ; 2 0000-0002-1340-8545 'Palmieri, G.' 3 ? 'Gogliettino, M.' 4 ? 'Agrillo, B.' 5 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country CH _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Int J Mol Sci' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1422-0067 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 22 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Key Physicochemical Determinants in the Antimicrobial Peptide RiLK1 Promote Amphipathic Structures.' _citation.year 2021 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.3390/ijms221810011 _citation.pdbx_database_id_PubMed 34576174 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Falcigno, L.' 1 0000-0002-3758-2716 primary ;D'Auria, G. ; 2 0000-0002-1340-8545 primary 'Palmieri, G.' 3 0000-0002-9007-4075 primary 'Gogliettino, M.' 4 ? primary 'Agrillo, B.' 5 ? primary 'Tate, R.' 6 ? primary 'Dardano, P.' 7 0000-0002-0616-3914 primary 'Nicolais, L.' 8 ? primary 'Balestrieri, M.' 9 0000-0003-4343-2148 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description RiLK1 _entity.formula_weight 1473.836 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'Decapeptide designed starting from IDR-1018 dodecapeptide, a synthetic derivative of bactenecin, a bovine host defense peptide.' # _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 RLKWVRIWRR _entity_poly.pdbx_seq_one_letter_code_can RLKWVRIWRR _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 ARG n 1 2 LEU n 1 3 LYS n 1 4 TRP n 1 5 VAL n 1 6 ARG n 1 7 ILE n 1 8 TRP n 1 9 ARG n 1 10 ARG 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 10 _pdbx_entity_src_syn.organism_scientific 'Bos taurus' _pdbx_entity_src_syn.organism_common_name Cattle _pdbx_entity_src_syn.ncbi_taxonomy_id 9913 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7OB2 _struct_ref.pdbx_db_accession 7OB2 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7OB2 _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 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7OB2 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _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 10 # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 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 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 1D 1 isotropic 2 1 1 '2D 1H-1H TOCSY' 1 isotropic 3 1 1 '2D 1H-1H NOESY' 1 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 4.2 _pdbx_nmr_exptl_sample_conditions.ionic_strength 'not defined' _pdbx_nmr_exptl_sample_conditions.details 'RiLK1 0.9 mM in SDS-d25 150 mM, 90% H2O, 10% D2O, pH 4.2, TSP' _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 'Not defined' _pdbx_nmr_exptl_sample_conditions.label conditions_1 _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '0.9 mM RiLK1, 150 mM 98% D SDS-d25, 90 % H2O, 10 % 98% D D2O, 90% H2O/10% D2O, SDS' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O, SDS' _pdbx_nmr_sample_details.label 'natural abundance' _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details 'RiLK1 0.9 mM in SDS-d25 150 mM, 90% H2O, 10% D2O, pH 4.2, TSP' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model '700 Unity Inova' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 700 _pdbx_nmr_spectrometer.details ? # _pdbx_nmr_refine.entry_id 7OB2 _pdbx_nmr_refine.method 'DGSA-distance geometry simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 6 # _pdbx_nmr_ensemble.entry_id 7OB2 _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'target function' _pdbx_nmr_ensemble.representative_conformer ? _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 7OB2 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'peak picking' CARA ? 'Keller and Wuthrich' 2 'chemical shift assignment' CARA ? 'Keller and Wuthrich' 4 'data analysis' CARA ? 'Keller and Wuthrich' 6 'structure calculation' CYANA ? 'Guntert, Mumenthaler and Wuthrich' # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7OB2 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7OB2 _struct.title 'NMR structure of the antimicrobial RiLK1 peptide in SDS micelles' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7OB2 _struct_keywords.text 'antimicrobial peptide, ANTIMICROBIAL PROTEIN' _struct_keywords.pdbx_keywords 'ANTIMICROBIAL 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 ? # _atom_sites.entry_id 7OB2 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _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 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # 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 ARG 1 1 1 ARG ARG A . n A 1 2 LEU 2 2 2 LEU LEU A . n A 1 3 LYS 3 3 3 LYS LYS A . n A 1 4 TRP 4 4 4 TRP TRP A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 ARG 6 6 6 ARG ARG A . n A 1 7 ILE 7 7 7 ILE ILE A . n A 1 8 TRP 8 8 8 TRP TRP A . n A 1 9 ARG 9 9 9 ARG ARG A . n A 1 10 ARG 10 10 10 ARG ARG A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 1780 ? # _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 ? _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 2021-11-17 2 'Structure model' 1 1 2023-06-14 # _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 ? # _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 Other # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category pdbx_database_status # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 2 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.solution_id _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 1 RiLK1 0.9 ? mM 'natural abundance' 1 SDS-d25 150 ? mM '98% D' 1 H2O 90 ? % 'natural abundance' 1 D2O 10 ? % '98% D' # 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 LEU A 2 ? ? -175.96 58.89 2 1 VAL A 5 ? ? -151.38 -41.76 3 1 ARG A 9 ? ? -176.33 62.30 4 2 LEU A 2 ? ? 179.60 60.53 5 2 VAL A 5 ? ? -151.37 -41.74 6 2 ARG A 9 ? ? -176.35 62.26 7 3 LEU A 2 ? ? 179.59 60.50 8 3 VAL A 5 ? ? -151.40 -41.81 9 3 ARG A 9 ? ? -176.32 62.19 10 4 LEU A 2 ? ? -175.98 58.88 11 4 VAL A 5 ? ? -151.37 -41.78 12 4 ARG A 9 ? ? -176.37 62.27 13 5 LEU A 2 ? ? 179.61 60.40 14 5 VAL A 5 ? ? -151.41 -41.75 15 5 ARG A 9 ? ? -176.28 62.19 16 6 LEU A 2 ? ? -176.04 58.89 17 6 VAL A 5 ? ? -151.40 -41.83 18 6 ARG A 9 ? ? -176.31 62.38 19 7 LEU A 2 ? ? -176.00 58.90 20 7 VAL A 5 ? ? -151.37 -41.72 21 7 TRP A 8 ? ? -48.88 153.00 22 7 ARG A 9 ? ? -176.27 62.19 23 8 LEU A 2 ? ? -176.01 58.88 24 8 VAL A 5 ? ? -151.41 -41.76 25 8 ARG A 9 ? ? -176.36 62.18 26 9 LEU A 2 ? ? -175.97 58.99 27 9 VAL A 5 ? ? -151.36 -41.84 28 9 ARG A 9 ? ? -176.34 62.21 29 10 LEU A 2 ? ? -176.07 58.88 30 10 VAL A 5 ? ? -151.28 -41.80 31 10 ARG A 9 ? ? -176.28 62.19 32 11 LEU A 2 ? ? -179.29 60.24 33 11 VAL A 5 ? ? -151.48 -41.75 34 11 ARG A 9 ? ? -176.31 62.31 35 12 LEU A 2 ? ? 179.58 60.48 36 12 VAL A 5 ? ? -151.36 -41.63 37 12 ARG A 9 ? ? -176.36 62.23 38 13 LEU A 2 ? ? -175.98 58.92 39 13 VAL A 5 ? ? -151.35 -41.77 40 13 TRP A 8 ? ? -48.99 150.98 41 13 ARG A 9 ? ? -176.37 62.21 42 14 LEU A 2 ? ? -161.55 54.00 43 14 VAL A 5 ? ? -151.31 -41.75 44 14 ARG A 9 ? ? -176.35 62.27 45 15 LEU A 2 ? ? -176.01 58.89 46 15 VAL A 5 ? ? -151.37 -41.78 47 15 ARG A 9 ? ? -176.36 62.29 48 16 LEU A 2 ? ? -176.03 58.93 49 16 VAL A 5 ? ? -151.44 -41.76 50 16 ARG A 9 ? ? -176.31 62.17 51 17 LEU A 2 ? ? -176.04 58.99 52 17 VAL A 5 ? ? -151.41 -41.81 53 17 TRP A 8 ? ? -49.06 151.62 54 17 ARG A 9 ? ? -179.34 64.87 55 18 LEU A 2 ? ? 179.60 60.49 56 18 VAL A 5 ? ? -151.41 -41.75 57 18 TRP A 8 ? ? -49.08 151.55 58 18 ARG A 9 ? ? 179.17 65.29 59 19 LEU A 2 ? ? -179.32 60.32 60 19 VAL A 5 ? ? -151.51 -41.76 61 19 ARG A 9 ? ? -176.32 62.23 62 20 LEU A 2 ? ? -176.08 58.97 63 20 LYS A 3 ? ? -156.59 22.61 64 20 VAL A 5 ? ? -151.54 -41.83 65 20 ARG A 9 ? ? -176.35 62.31 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #