data_2YOM # _entry.id 2YOM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.315 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2YOM PDBE EBI-54585 WWPDB D_1290054585 BMRB 18159 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 2YON unspecified . BMRB 18159 unspecified . # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2YOM _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2012-10-25 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Rani, R.' 1 'Lecher, J.' 2 'Hartmann, R.' 3 'Krauss, U.' 4 'Jaeger, K.' 5 'Willbold, D.' 6 # _citation.id primary _citation.title ;Conservation of Dark Recovery Kinetic Parameters and Structural Features in the Pseudomonadaceae "Short" Light, Oxygen, Voltage (Lov) Protein Family: Implications for the Design of Lov-Based Optogenetic Tools. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 52 _citation.page_first 4460 _citation.page_last ? _citation.year 2013 _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 23746326 _citation.pdbx_database_id_DOI 10.1021/BI400311R # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Rani, R.' 1 ? primary 'Jentzsch, K.' 2 ? primary 'Lecher, J.' 3 ? primary 'Hartmann, R.' 4 ? primary 'Willbold, D.' 5 ? primary 'Jaeger, K.' 6 ? primary 'Krauss, U.' 7 ? # _cell.entry_id 2YOM _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YOM _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'SENSORY BOX PROTEIN' _entity.formula_weight 2781.132 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'JALPHA HELIX, RESIDUES 120-142' _entity.details 'N-TERMINAL ACETYLATION' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(ACE)SRQVELERELAELRARPKPDERA' _entity_poly.pdbx_seq_one_letter_code_can XSRQVELERELAELRARPKPDERA _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 ACE n 1 2 SER n 1 3 ARG n 1 4 GLN n 1 5 VAL n 1 6 GLU n 1 7 LEU n 1 8 GLU n 1 9 ARG n 1 10 GLU n 1 11 LEU n 1 12 ALA n 1 13 GLU n 1 14 LEU n 1 15 ARG n 1 16 ALA n 1 17 ARG n 1 18 PRO n 1 19 LYS n 1 20 PRO n 1 21 ASP n 1 22 GLU n 1 23 ARG n 1 24 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 'PSEUDOMONAS PUTIDA KT2440' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 160488 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q88E39_PSEPK _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession Q88E39 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2YOM _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 24 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q88E39 _struct_ref_seq.db_align_beg 120 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 142 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 120 _struct_ref_seq.pdbx_auth_seq_align_end 142 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2YOM _struct_ref_seq_dif.mon_id ACE _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q88E39 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details acetylation _struct_ref_seq_dif.pdbx_auth_seq_num 119 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 ACE non-polymer . 'ACETYL GROUP' ? 'C2 H4 O' 44.053 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 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 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 # _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.type NOESY _pdbx_nmr_exptl.solution_id 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298.0 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1.0 _pdbx_nmr_exptl_sample_conditions.pH 6.3 _pdbx_nmr_exptl_sample_conditions.ionic_strength 150 _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '10% TRIFLUOROETHANOL/10% D2O/80% WATER' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model VNMRS _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 900 # _pdbx_nmr_refine.entry_id 2YOM _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details 'REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2YOM _pdbx_nmr_details.text ;THE STRUCTURE WAS DETERMINED FROM PARTIAL MANUALLY ASSIGNED 1H-1H NOESY DATA OF SYNTHETIC PEPTIDE, ASSISTED BY AUTOMATED ASSIGNMENTS BY ARIA AND CALCULATED WITH CNS. ; # _pdbx_nmr_ensemble.entry_id 2YOM _pdbx_nmr_ensemble.conformers_calculated_total_number 250 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'LOWEST ENERGY' # _pdbx_nmr_representative.entry_id 2YOM _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria ? # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement CNS 1.21 'BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARREN' 1 'structure solution' ARIA 2.3.1 ? 2 'structure solution' 'CcpNmr Analysis' 2.2 ? 3 'structure solution' 'CcpNmr Analysis' 2.1 ? 4 'structure solution' NMRPipe 7.3.2012.114.11.33 ? 5 'structure solution' VnmrJ 2.3A ? 6 # _exptl.entry_id 2YOM _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2YOM _struct.title ;Solution NMR structure of the C-terminal extension of two bacterial light, oxygen, voltage (LOV) photoreceptor proteins from Pseudomonas putida ; _struct.pdbx_descriptor 'SENSORY BOX PROTEIN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2YOM _struct_keywords.pdbx_keywords 'SIGNALING PROTEIN' _struct_keywords.text 'SIGNALING PROTEIN, PHOTORECEPTOR' # _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_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id SER _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 2 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ARG _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 17 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id SER _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 120 _struct_conf.end_auth_comp_id ARG _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 135 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 16 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_conn.id covale1 _struct_conn.conn_type_id covale _struct_conn.pdbx_leaving_atom_flag both _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_comp_id ACE _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_label_atom_id C _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 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_comp_id SER _struct_conn.ptnr2_label_seq_id 2 _struct_conn.ptnr2_label_atom_id N _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ACE _struct_conn.ptnr1_auth_seq_id 119 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id SER _struct_conn.ptnr2_auth_seq_id 120 _struct_conn.ptnr2_symmetry 1_555 _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 1.333 _struct_conn.pdbx_value_order ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 2YOM _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 2YOM _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 ACE 1 119 119 ACE ACE A . n A 1 2 SER 2 120 120 SER SER A . n A 1 3 ARG 3 121 121 ARG ARG A . n A 1 4 GLN 4 122 122 GLN GLN A . n A 1 5 VAL 5 123 123 VAL VAL A . n A 1 6 GLU 6 124 124 GLU GLU A . n A 1 7 LEU 7 125 125 LEU LEU A . n A 1 8 GLU 8 126 126 GLU GLU A . n A 1 9 ARG 9 127 127 ARG ARG A . n A 1 10 GLU 10 128 128 GLU GLU A . n A 1 11 LEU 11 129 129 LEU LEU A . n A 1 12 ALA 12 130 130 ALA ALA A . n A 1 13 GLU 13 131 131 GLU GLU A . n A 1 14 LEU 14 132 132 LEU LEU A . n A 1 15 ARG 15 133 133 ARG ARG A . n A 1 16 ALA 16 134 134 ALA ALA A . n A 1 17 ARG 17 135 135 ARG ARG A . n A 1 18 PRO 18 136 136 PRO PRO A . n A 1 19 LYS 19 137 137 LYS LYS A . n A 1 20 PRO 20 138 138 PRO PRO A . n A 1 21 ASP 21 139 139 ASP ASP A . n A 1 22 GLU 22 140 140 GLU GLU A . n A 1 23 ARG 23 141 141 ARG ARG A . n A 1 24 ALA 24 142 142 ALA ALA 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 # _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 2013-07-10 2 'Structure model' 1 1 2013-07-17 3 'Structure model' 1 2 2016-05-04 4 'Structure model' 1 3 2019-10-23 # _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' 'Atomic model' 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' Other 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Derived calculations' 8 4 '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 4 'Structure model' pdbx_database_status 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' struct_conn 4 4 'Structure model' struct_ref_seq_dif # 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' '_pdbx_database_status.status_code_cs' 2 4 'Structure model' '_pdbx_database_status.status_code_mr' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_ref_seq_dif.details' # 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 GLU A 140 ? ? 62.24 76.22 2 2 PRO A 138 ? ? -88.79 43.78 3 2 ASP A 139 ? ? -106.69 56.57 4 3 PRO A 138 ? ? -80.33 49.62 5 4 ASP A 139 ? ? -169.02 82.53 6 4 ARG A 141 ? ? 71.54 -55.64 7 6 ASP A 139 ? ? 56.42 79.53 8 8 ASP A 139 ? ? 62.48 85.81 9 10 PRO A 138 ? ? -77.30 48.36 10 10 GLU A 140 ? ? -97.19 59.11 #