data_2MLV # _entry.id 2MLV # _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 2MLV RCSB RCSB103769 BMRB 19833 WWPDB D_1000103769 # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 19833 BMRB unspecified . 2MLU PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2MLV _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-03-05 _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 REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kristiansen, P.' 1 'Ovchinnikov, K.' 2 'Diep, D.' 3 # _citation.id primary _citation.title 'Defining the Structure and Receptor Binding Domain of the Leaderless Bacteriocin LsbB.' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 289 _citation.page_first 23838 _citation.page_last 23845 _citation.year 2014 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24993828 _citation.pdbx_database_id_DOI 10.1074/jbc.M114.579698 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Ovchinnikov, K.V.' 1 primary 'Kristiansen, P.E.' 2 primary 'Uzelac, G.' 3 primary 'Topisirovic, L.' 4 primary 'Kojic, M.' 5 primary 'Nissen-Meyer, J.' 6 primary 'Nes, I.F.' 7 primary 'Diep, D.B.' 8 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description LsbB _entity.formula_weight 3418.022 _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 MKTILRFVAGYDIASHKKKTGGYPWERGKA _entity_poly.pdbx_seq_one_letter_code_can MKTILRFVAGYDIASHKKKTGGYPWERGKA _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 THR n 1 4 ILE n 1 5 LEU n 1 6 ARG n 1 7 PHE n 1 8 VAL n 1 9 ALA n 1 10 GLY n 1 11 TYR n 1 12 ASP n 1 13 ILE n 1 14 ALA n 1 15 SER n 1 16 HIS n 1 17 LYS n 1 18 LYS n 1 19 LYS n 1 20 THR n 1 21 GLY n 1 22 GLY n 1 23 TYR n 1 24 PRO n 1 25 TRP n 1 26 GLU n 1 27 ARG n 1 28 GLY n 1 29 LYS n 1 30 ALA 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 'Lactococcus lactis subsp. lactis' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 1360 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q7X2B5_LACLL _struct_ref.pdbx_db_accession Q7X2B5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code MKTILRFVAGYDIASHKKKTGGYPWERGKA _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 2MLV _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 30 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q7X2B5 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 30 _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 30 # 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 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 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 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 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-15N HSQC' 1 2 1 '2D DQF-COSY' 1 3 1 '2D 1H-1H TOCSY' 1 4 1 '2D 1H-13C HSQC' 1 5 1 '2D 1H-1H NOESY' 1 6 1 '2D 1H-13C HMBC' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH ? _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '1.0 mM LsbB, 0.2 mM DSS, 50% H2O, 50% [U-99% 2H] TFE' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system trifluoroethanol/water # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model Avance _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2MLV _pdbx_nmr_refine.method 'torsion angle dynamics' _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 2MLV _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.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2MLV _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA 2.0 1 Goddard 'peak picking' SPARKY ? 2 'Cornilescu, Delaglio and Bax' 'data analysis' TALOS + 3 'Keller and Wuthrich' 'chemical shift assignment' CARA ? 4 'Bruker Biospin' collection TOPSPIN 2.4 5 'Guntert, Mumenthaler and Wuthrich' refinement CYANA ? 6 # _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 'Structure-function studies of LsbB' _exptl.entry_id 2MLV _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2MLV _struct.title 'Structure of the antimicrobial peptide LsbB in TFE/water' _struct.pdbx_descriptor LsbB _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2MLV _struct_keywords.pdbx_keywords 'ANTIMICROBIAL PROTEIN' _struct_keywords.text 'Bacteriocin, antimicrobial peptide, receptor binding domain, mode of killing, TFE, 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 ? # _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 ILE _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 LYS _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 18 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ILE _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 4 _struct_conf.end_auth_comp_id LYS _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 18 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 15 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2MLV _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 THR 3 3 3 THR THR A . n A 1 4 ILE 4 4 4 ILE ILE A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 ARG 6 6 6 ARG ARG A . n A 1 7 PHE 7 7 7 PHE PHE A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 ALA 9 9 9 ALA ALA A . n A 1 10 GLY 10 10 10 GLY GLY A . n A 1 11 TYR 11 11 11 TYR TYR A . n A 1 12 ASP 12 12 12 ASP ASP A . n A 1 13 ILE 13 13 13 ILE ILE A . n A 1 14 ALA 14 14 14 ALA ALA A . n A 1 15 SER 15 15 15 SER SER A . n A 1 16 HIS 16 16 16 HIS HIS A . n A 1 17 LYS 17 17 17 LYS LYS A . n A 1 18 LYS 18 18 18 LYS LYS A . n A 1 19 LYS 19 19 19 LYS LYS A . n A 1 20 THR 20 20 20 THR THR A . n A 1 21 GLY 21 21 21 GLY GLY A . n A 1 22 GLY 22 22 22 GLY GLY A . n A 1 23 TYR 23 23 23 TYR TYR A . n A 1 24 PRO 24 24 24 PRO PRO A . n A 1 25 TRP 25 25 25 TRP TRP A . n A 1 26 GLU 26 26 26 GLU GLU A . n A 1 27 ARG 27 27 27 ARG ARG A . n A 1 28 GLY 28 28 28 GLY GLY A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 ALA 30 30 30 ALA ALA 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 2014-07-16 2 'Structure model' 1 1 2014-07-23 3 'Structure model' 1 2 2014-09-10 # _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 ? # 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' 'Database references' 2 3 'Structure model' 'Database references' # 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 LsbB-1 1.0 ? mM ? 1 DSS-2 0.2 ? mM ? 1 H2O-3 50 ? % ? 1 TFE-4 50 ? % '[U-99% 2H]' 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 LYS A 19 ? ? 55.93 88.39 2 1 GLU A 26 ? ? -95.52 46.80 3 2 THR A 3 ? ? -140.68 33.28 4 2 LYS A 19 ? ? 61.21 91.35 5 2 GLU A 26 ? ? -95.53 42.31 6 3 LYS A 19 ? ? 55.47 83.84 7 3 GLU A 26 ? ? -94.67 47.68 8 3 LYS A 29 ? ? 52.52 74.50 9 4 LYS A 19 ? ? 60.77 82.14 10 4 GLU A 26 ? ? -95.41 46.65 11 5 LYS A 19 ? ? 58.78 80.24 12 5 GLU A 26 ? ? -95.64 38.24 13 6 THR A 3 ? ? -95.51 34.92 14 6 LYS A 19 ? ? 58.75 89.02 15 6 GLU A 26 ? ? -95.69 44.20 16 7 LYS A 19 ? ? 56.17 87.84 17 7 GLU A 26 ? ? -95.56 46.66 18 8 LYS A 19 ? ? 60.96 91.60 19 8 GLU A 26 ? ? -94.87 45.42 20 8 ARG A 27 ? ? -99.19 36.94 21 9 THR A 3 ? ? -99.84 31.65 22 9 LYS A 19 ? ? 53.14 85.62 23 9 GLU A 26 ? ? -95.64 43.35 24 10 THR A 3 ? ? -97.56 34.33 25 10 LYS A 19 ? ? 54.54 85.99 26 10 GLU A 26 ? ? -95.62 46.51 27 11 THR A 3 ? ? -95.58 32.85 28 11 LYS A 19 ? ? 54.24 84.03 29 11 GLU A 26 ? ? -94.39 47.48 30 11 LYS A 29 ? ? -95.96 54.03 31 12 THR A 3 ? ? -98.22 42.14 32 12 LYS A 19 ? ? 54.85 85.48 33 12 GLU A 26 ? ? -95.52 47.18 34 13 THR A 3 ? ? -96.28 34.25 35 13 LYS A 19 ? ? 57.90 87.75 36 13 THR A 20 ? ? -178.89 149.37 37 13 GLU A 26 ? ? -95.51 46.69 38 14 LYS A 19 ? ? 59.02 89.28 39 14 GLU A 26 ? ? -95.04 44.72 40 15 THR A 3 ? ? -97.50 33.01 41 15 LYS A 19 ? ? 56.99 89.21 42 15 GLU A 26 ? ? -95.58 45.51 43 16 LYS A 19 ? ? 57.81 89.05 44 16 GLU A 26 ? ? -94.98 40.34 45 17 THR A 3 ? ? -158.95 40.69 46 17 LYS A 19 ? ? 54.86 88.84 47 17 GLU A 26 ? ? -95.20 44.62 48 18 LYS A 19 ? ? 55.54 86.11 49 18 THR A 20 ? ? -177.92 147.58 50 18 GLU A 26 ? ? -95.59 47.29 51 19 THR A 3 ? ? -96.27 34.36 52 19 LYS A 19 ? ? 53.54 85.78 53 19 LYS A 29 ? ? 52.61 71.28 54 20 LYS A 19 ? ? 62.11 91.24 55 20 GLU A 26 ? ? -94.29 42.15 #