data_2LWS # _entry.id 2LWS # _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 2LWS pdb_00002lws 10.2210/pdb2lws/pdb RCSB RCSB102929 ? ? BMRB 18643 ? ? WWPDB D_1000102929 ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 18643 BMRB unspecified . 2LWQ PDB unspecified . 2LWT PDB unspecified . 2LWU PDB unspecified . 2LWV PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LWS _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-08-06 _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 _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Elliott, A.G.' 1 'Mylne, J.S.' 2 'Rosengren, K.' 3 # _citation.id primary _citation.title 'Evolutionary origins of a bioactive peptide buried within Preproalbumin.' _citation.journal_abbrev 'Plant Cell' _citation.journal_volume 26 _citation.page_first 981 _citation.page_last 995 _citation.year 2014 _citation.journal_id_ASTM PLCEEW _citation.country US _citation.journal_id_ISSN 1040-4651 _citation.journal_id_CSD 2109 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24681618 _citation.pdbx_database_id_DOI 10.1105/tpc.114.123620 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Elliott, A.G.' 1 ? primary 'Delay, C.' 2 ? primary 'Liu, H.' 3 ? primary 'Phua, Z.' 4 ? primary 'Rosengren, K.J.' 5 ? primary 'Benfield, A.H.' 6 ? primary 'Panero, J.L.' 7 ? primary 'Colgrave, M.L.' 8 ? primary 'Jayasena, A.S.' 9 ? primary 'Dunse, K.M.' 10 ? primary 'Anderson, M.A.' 11 ? primary 'Schilling, E.E.' 12 ? primary 'Ortiz-Barrientos, D.' 13 ? primary 'Craik, D.J.' 14 ? primary 'Mylne, J.S.' 15 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'PawS Derived Peptide 4 (PDP-4)' _entity.formula_weight 1367.557 _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 GSCFGAFCFRRD _entity_poly.pdbx_seq_one_letter_code_can GSCFGAFCFRRD _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 GLY n 1 2 SER n 1 3 CYS n 1 4 PHE n 1 5 GLY n 1 6 ALA n 1 7 PHE n 1 8 CYS n 1 9 PHE n 1 10 ARG n 1 11 ARG n 1 12 ASP n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2LWS _struct_ref.pdbx_db_accession 2LWS _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2LWS _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 2LWS _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _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 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 # 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 DQF-COSY' 1 3 1 '2D 1H-1H NOESY' 1 4 2 '2D 1H-1H TOCSY' 1 5 2 '2D 1H-1H NOESY' 1 6 2 '2D 1H-13C HSQC' 1 7 2 '2D 1H-1H ECOSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0 _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 280 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '5 mg/mL PDP-4, 80% H2O/10% D2O/10% DMSO' 1 '80% H2O/10% D2O/10% DMSO' '5 mg/mL PDP-4, 90% D2O / 10% DMSO' 2 '90% D2O / 10% DMSO' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 600 Bruker AVANCE 1 'Bruker Avance' 500 Bruker AVANCE 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2LWS _pdbx_nmr_refine.method 'simulated annealing, 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 'target function, favourable non-bonded energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LWS _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 2LWS _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 'Bruker Biospin' collection TopSpin 3.0 1 'Bruker Biospin' processing TopSpin 3.0 2 'Bartels et al.' 'data analysis' XEASY ? 3 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA 3.0 4 'Guntert, Mumenthaler and Wuthrich' refinement CYANA ? 5 # _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 2LWS _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LWS _struct.title 'NMR solution structure of PawS Derived Peptide 4 (PDP-4)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LWS _struct_keywords.pdbx_keywords 'PLANT PROTEIN' _struct_keywords.text 'plant peptide, PawS derived, cyclic peptide, PLANT 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 PHE _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 CYS _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 8 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id PHE _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 4 _struct_conf.end_auth_comp_id CYS _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 8 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 3 SG ? ? ? 1_555 A CYS 8 SG ? ? A CYS 3 A CYS 8 1_555 ? ? ? ? ? ? ? 1.984 ? ? covale1 covale both ? A GLY 1 N ? ? ? 1_555 A ASP 12 C ? ? A GLY 1 A ASP 12 1_555 ? ? ? ? ? ? ? 1.336 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _atom_sites.entry_id 2LWS _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 GLY 1 1 1 GLY GLY A . n A 1 2 SER 2 2 2 SER SER A . n A 1 3 CYS 3 3 3 CYS CYS 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 ALA 6 6 6 ALA ALA A . n A 1 7 PHE 7 7 7 PHE PHE A . n A 1 8 CYS 8 8 8 CYS CYS A . n A 1 9 PHE 9 9 9 PHE PHE A . n A 1 10 ARG 10 10 10 ARG ARG A . n A 1 11 ARG 11 11 11 ARG ARG A . n A 1 12 ASP 12 12 12 ASP ASP A . n # _pdbx_molecule_features.prd_id PRD_000874 _pdbx_molecule_features.name 'PawS Derived Peptide 4 (PDP-4)' _pdbx_molecule_features.type 'Cyclic peptide' _pdbx_molecule_features.class 'Enzyme inhibitor' _pdbx_molecule_features.details ? # _pdbx_molecule.instance_id 1 _pdbx_molecule.prd_id PRD_000874 _pdbx_molecule.asym_id A # _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 2013-08-21 2 'Structure model' 1 1 2016-06-01 3 'Structure model' 1 2 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 ? # 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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other # 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 3 'Structure model' database_2 2 3 'Structure model' pdbx_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' pdbx_nmr_spectrometer 5 3 'Structure model' struct_conn # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 3 'Structure model' '_pdbx_nmr_software.name' 5 3 'Structure model' '_pdbx_nmr_spectrometer.model' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # 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 PDP-4-1 5 ? mg/mL ? 1 PDP-4-2 5 ? mg/mL ? 2 # 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 SER A 2 ? ? -90.97 46.06 2 1 PHE A 4 ? ? -150.10 79.80 3 2 SER A 2 ? ? -90.94 46.14 4 3 SER A 2 ? ? -90.95 46.02 5 3 PHE A 4 ? ? -150.11 79.83 6 4 SER A 2 ? ? -91.04 45.97 7 4 PHE A 4 ? ? -150.15 79.77 8 5 SER A 2 ? ? -90.73 45.74 9 5 PHE A 4 ? ? -150.16 79.88 10 5 ARG A 11 ? ? -90.38 48.02 11 6 SER A 2 ? ? -90.87 45.97 12 6 PHE A 4 ? ? -150.10 79.87 13 7 SER A 2 ? ? -90.91 45.98 14 7 PHE A 4 ? ? -150.14 79.87 15 8 SER A 2 ? ? -90.85 45.94 16 8 PHE A 4 ? ? -150.17 80.00 17 9 SER A 2 ? ? -90.98 46.04 18 9 PHE A 4 ? ? -150.12 79.93 19 10 SER A 2 ? ? -90.93 46.05 20 10 PHE A 4 ? ? -150.18 80.01 21 11 SER A 2 ? ? -90.88 45.87 22 11 PHE A 4 ? ? -150.16 80.00 23 11 PHE A 9 ? ? -119.89 66.30 24 12 SER A 2 ? ? -91.02 45.95 25 12 PHE A 4 ? ? -150.11 79.95 26 12 ARG A 11 ? ? -97.48 56.62 27 13 SER A 2 ? ? -90.98 46.04 28 13 PHE A 4 ? ? -150.14 79.92 29 13 ARG A 11 ? ? -92.01 50.22 30 14 SER A 2 ? ? -90.91 45.95 31 14 PHE A 4 ? ? -150.08 79.73 32 14 ARG A 11 ? ? -95.75 53.12 33 15 SER A 2 ? ? -90.95 45.92 34 15 PHE A 4 ? ? -150.10 79.63 35 15 ARG A 11 ? ? -96.35 39.97 36 16 SER A 2 ? ? -91.01 41.62 37 16 PHE A 4 ? ? -150.24 79.60 38 16 ARG A 11 ? ? -104.73 61.76 39 17 SER A 2 ? ? -90.96 41.49 40 17 PHE A 4 ? ? -150.06 79.69 41 17 ARG A 11 ? ? -106.44 61.07 42 18 SER A 2 ? ? -90.85 41.47 43 18 PHE A 4 ? ? -150.14 79.80 44 19 SER A 2 ? ? -90.96 41.47 45 19 PHE A 4 ? ? -150.18 79.84 46 20 SER A 2 ? ? -90.98 41.50 47 20 PHE A 4 ? ? -150.22 79.77 48 20 PHE A 9 ? ? -119.95 65.54 49 20 ARG A 11 ? ? -96.67 46.53 #