data_1QZB # _entry.id 1QZB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1QZB pdb_00001qzb 10.2210/pdb1qzb/pdb RCSB RCSB020252 ? ? WWPDB D_1000020252 ? ? # 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 2003-11-04 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Refinement description' # 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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' em_3d_fitting_list 5 4 'Structure model' em_image_scans 6 4 'Structure model' pdbx_initial_refinement_model # 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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_em_3d_fitting_list.accession_code' 4 4 'Structure model' '_em_3d_fitting_list.initial_refinement_model_id' 5 4 'Structure model' '_em_3d_fitting_list.source_name' 6 4 'Structure model' '_em_3d_fitting_list.type' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1QZB _pdbx_database_status.recvd_initial_deposition_date 2003-09-16 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1OB2 'E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA' unspecified PDB 1QZA 'Coordinates of the A/T site tRNA model fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome' unspecified PDB 1QZC ;Coordinates of S12, SH44, LH69 and SRL separately fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome ; unspecified PDB 1QZD 'EF-Tu.kirromycin coordinates fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome' unspecified PDB 1R2W 'COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM MAP OF THE 70S RIBOSOME' unspecified PDB 1R2X 'COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME' unspecified EMDB EMD-1056 . 'associated EM volume' # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Valle, M.' 1 'Zavialov, A.' 2 'Li, W.' 3 'Stagg, S.M.' 4 'Sengupta, J.' 5 'Nielsen, R.C.' 6 'Nissen, P.' 7 'Harvey, S.C.' 8 'Ehrenberg, M.' 9 'Frank, J.' 10 # _citation.id primary _citation.title 'Incorporation of Aminoacyl-tRNA into the Ribosome as seen by Cryo-electron Microscopy' _citation.journal_abbrev Nat.Struct.Biol. _citation.journal_volume 10 _citation.page_first 899 _citation.page_last 906 _citation.year 2003 _citation.journal_id_ASTM NSBIEW _citation.country US _citation.journal_id_ISSN 1072-8368 _citation.journal_id_CSD 2024 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14566331 _citation.pdbx_database_id_DOI 10.1038/nsb1003 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Valle, M.' 1 ? primary 'Zavialov, A.' 2 ? primary 'Li, W.' 3 ? primary 'Stagg, S.M.' 4 ? primary 'Sengupta, J.' 5 ? primary 'Nielsen, R.C.' 6 ? primary 'Nissen, P.' 7 ? primary 'Harvey, S.C.' 8 ? primary 'Ehrenberg, M.' 9 ? primary 'Frank, J.' 10 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description Phe-tRNA _entity.formula_weight 24518.570 _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 polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA _entity_poly.pdbx_seq_one_letter_code_can GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA _entity_poly.pdbx_strand_id B _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 G n 1 2 C n 1 3 G n 1 4 G n 1 5 A n 1 6 U n 1 7 U n 1 8 U n 1 9 A n 1 10 G n 1 11 C n 1 12 U n 1 13 C n 1 14 A n 1 15 G n 1 16 U n 1 17 U n 1 18 G n 1 19 G n 1 20 G n 1 21 A n 1 22 G n 1 23 A n 1 24 G n 1 25 C n 1 26 G n 1 27 C n 1 28 C n 1 29 A n 1 30 G n 1 31 A n 1 32 C n 1 33 U n 1 34 G n 1 35 A n 1 36 A n 1 37 G n 1 38 A n 1 39 U n 1 40 C n 1 41 U n 1 42 G n 1 43 G n 1 44 A n 1 45 G n 1 46 G n 1 47 U n 1 48 C n 1 49 C n 1 50 U n 1 51 G n 1 52 U n 1 53 G n 1 54 U n 1 55 U n 1 56 C n 1 57 G n 1 58 A n 1 59 U n 1 60 C n 1 61 C n 1 62 A n 1 63 C n 1 64 A n 1 65 G n 1 66 A n 1 67 A n 1 68 U n 1 69 U n 1 70 C n 1 71 G n 1 72 C n 1 73 A n 1 74 C n 1 75 C n 1 76 A n # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 G 1 1 ? ? ? B . n A 1 2 C 2 2 2 C C B . n A 1 3 G 3 3 3 G G B . n A 1 4 G 4 4 4 G G B . n A 1 5 A 5 5 5 A A B . n A 1 6 U 6 6 6 U U B . n A 1 7 U 7 7 7 U U B . n A 1 8 U 8 8 8 U U B . n A 1 9 A 9 9 9 A A B . n A 1 10 G 10 10 10 G G B . n A 1 11 C 11 11 11 C C B . n A 1 12 U 12 12 12 U U B . n A 1 13 C 13 13 13 C C B . n A 1 14 A 14 14 14 A A B . n A 1 15 G 15 15 15 G G B . n A 1 16 U 16 16 16 U U B . n A 1 17 U 17 17 17 U U B . n A 1 18 G 18 18 18 G G B . n A 1 19 G 19 19 19 G G B . n A 1 20 G 20 20 20 G G B . n A 1 21 A 21 21 21 A A B . n A 1 22 G 22 22 22 G G B . n A 1 23 A 23 23 23 A A B . n A 1 24 G 24 24 24 G G B . n A 1 25 C 25 25 25 C C B . n A 1 26 G 26 26 26 G G B . n A 1 27 C 27 27 27 C C B . n A 1 28 C 28 28 28 C C B . n A 1 29 A 29 29 29 A A B . n A 1 30 G 30 30 30 G G B . n A 1 31 A 31 31 31 A A B . n A 1 32 C 32 32 32 C C B . n A 1 33 U 33 33 33 U U B . n A 1 34 G 34 34 34 G G B . n A 1 35 A 35 35 35 A A B . n A 1 36 A 36 36 36 A A B . n A 1 37 G 37 37 37 G G B . n A 1 38 A 38 38 38 A A B . n A 1 39 U 39 39 39 U U B . n A 1 40 C 40 40 40 C C B . n A 1 41 U 41 41 41 U U B . n A 1 42 G 42 42 42 G G B . n A 1 43 G 43 43 43 G G B . n A 1 44 A 44 44 44 A A B . n A 1 45 G 45 45 45 G G B . n A 1 46 G 46 46 46 G G B . n A 1 47 U 47 47 47 U U B . n A 1 48 C 48 48 48 C C B . n A 1 49 C 49 49 49 C C B . n A 1 50 U 50 50 50 U U B . n A 1 51 G 51 51 51 G G B . n A 1 52 U 52 52 52 U U B . n A 1 53 G 53 53 53 G G B . n A 1 54 U 54 54 54 U U B . n A 1 55 U 55 55 55 U U B . n A 1 56 C 56 56 56 C C B . n A 1 57 G 57 57 57 G G B . n A 1 58 A 58 58 58 A A B . n A 1 59 U 59 59 59 U U B . n A 1 60 C 60 60 60 C C B . n A 1 61 C 61 61 61 C C B . n A 1 62 A 62 62 62 A A B . n A 1 63 C 63 63 63 C C B . n A 1 64 A 64 64 64 A A B . n A 1 65 G 65 65 65 G G B . n A 1 66 A 66 66 66 A A B . n A 1 67 A 67 67 67 A A B . n A 1 68 U 68 68 68 U U B . n A 1 69 U 69 69 69 U U B . n A 1 70 C 70 70 70 C C B . n A 1 71 G 71 71 71 G G B . n A 1 72 C 72 72 72 C C B . n A 1 73 A 73 73 73 A A B . n A 1 74 C 74 74 74 C C B . n A 1 75 C 75 75 75 C C B . n A 1 76 A 76 76 76 A A B . n # _cell.entry_id 1QZB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.pdbx_unique_axis ? _cell.Z_PDB 1 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 1QZB _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 1 _symmetry.cell_setting ? # _exptl.entry_id 1QZB _exptl.method 'ELECTRON MICROSCOPY' _exptl.crystals_number ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 75 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 75 _refine_hist.d_res_high . _refine_hist.d_res_low . # _database_PDB_matrix.entry_id 1QZB _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 # _struct.entry_id 1QZB _struct.title 'Coordinates of the A-site tRNA model fitted into the cryo-EM map of 70S ribosome in the pre-translocational state' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1QZB _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'A-site tRNA, RNA' # _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_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1QZB _struct_ref.pdbx_db_accession 1QZB _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1QZB _struct_ref_seq.pdbx_strand_id B _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 76 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1QZB _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 76 _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 76 # _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 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # _pdbx_database_remark.id 999 _pdbx_database_remark.text ;SEQUENCE THE STRUCTURE CONTAINS P ATOMS ONLY ; # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 1QZB _em_3d_fitting.ref_protocol OTHER _em_3d_fitting.ref_space REAL _em_3d_fitting.overall_b_value ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details 'METHOD--Manual fitting in O' _em_3d_fitting.method ? # _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.id 1 _em_3d_fitting_list.pdb_entry_id 1OB2 _em_3d_fitting_list.pdb_chain_id ? _em_3d_fitting_list.details ? _em_3d_fitting_list.initial_refinement_model_id 1 _em_3d_fitting_list.chain_id ? _em_3d_fitting_list.chain_residue_range ? _em_3d_fitting_list.pdb_chain_residue_range ? _em_3d_fitting_list.source_name PDB _em_3d_fitting_list.type 'experimental model' _em_3d_fitting_list.accession_code 1OB2 # _em_3d_reconstruction.entry_id 1QZB _em_3d_reconstruction.id 1 _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.num_particles 52181 _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.method '3D projection matching; conjugate gradient with regularization' _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size 2.82 _em_3d_reconstruction.resolution 9 _em_3d_reconstruction.magnification_calibration TMV _em_3d_reconstruction.details 'SPIDER package' _em_3d_reconstruction.resolution_method ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.algorithm ? # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name 'Polymix buffer' _em_buffer.pH 7.5 _em_buffer.details 'Polymix buffer' # loop_ _em_entity_assembly.id _em_entity_assembly.name _em_entity_assembly.type _em_entity_assembly.parent_id _em_entity_assembly.synonym _em_entity_assembly.details _em_entity_assembly.oligomeric_details 1 '70S ribosome' RIBOSOME 0 ? ;70S bearing deacylated tRNAfMet in the P site and dipeptidyl MP-tRNA in the A site. Same complex as in project 138 but in the absence of Kirromicin. The Phe-tRNA is fully delivered to the A-site and after the peptide bond formation the dipeptidyl-tRNA stays in the A site. mRNA codes for MP-stop ; ? 2 tRNA ? 1 ? ? ? # _em_imaging.entry_id 1QZB _em_imaging.id 1 _em_imaging.specimen_id 1 _em_imaging.date ? _em_imaging.temperature 93 _em_imaging.microscope_model 'FEI TECNAI F20' _em_imaging.nominal_defocus_min 2000 _em_imaging.nominal_defocus_max 4000 _em_imaging.tilt_angle_min 0 _em_imaging.tilt_angle_max 0 _em_imaging.nominal_cs 2.0 _em_imaging.mode 'BRIGHT FIELD' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.nominal_magnification 50000 _em_imaging.calibrated_magnification 49696 _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.accelerating_voltage 200 _em_imaging.details ? _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.citation_id ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details 'Quantifoil holley carbon film grids' _em_sample_support.film_material ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type ? _em_sample_support.method ? # _em_vitrification.entry_id 1QZB _em_vitrification.id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.details 'Rapid-freezing in liquid ethane' _em_vitrification.citation_id ? _em_vitrification.humidity ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.specimen_id 1 _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 1QZB _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' # _em_single_particle_entity.entry_id 1QZB _em_single_particle_entity.id 1 _em_single_particle_entity.point_symmetry C1 _em_single_particle_entity.image_processing_id 1 # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id B _pdbx_unobs_or_zero_occ_residues.auth_comp_id G _pdbx_unobs_or_zero_occ_residues.auth_seq_id 1 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id G _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 U OP3 O N N 111 U P P N N 112 U OP1 O N N 113 U OP2 O N N 114 U "O5'" O N N 115 U "C5'" C N N 116 U "C4'" C N R 117 U "O4'" O N N 118 U "C3'" C N S 119 U "O3'" O N N 120 U "C2'" C N R 121 U "O2'" O N N 122 U "C1'" C N R 123 U N1 N N N 124 U C2 C N N 125 U O2 O N N 126 U N3 N N N 127 U C4 C N N 128 U O4 O N N 129 U C5 C N N 130 U C6 C N N 131 U HOP3 H N N 132 U HOP2 H N N 133 U "H5'" H N N 134 U "H5''" H N N 135 U "H4'" H N N 136 U "H3'" H N N 137 U "HO3'" H N N 138 U "H2'" H N N 139 U "HO2'" H N N 140 U "H1'" H N N 141 U H3 H N N 142 U H5 H N N 143 U H6 H N N 144 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # _em_ctf_correction.id 1 _em_ctf_correction.details 'CTF correction of 3D maps by Wiener filteration' _em_ctf_correction.type . # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.details ? _em_image_recording.id 1 _em_image_recording.avg_electron_dose_per_image 20 _em_image_recording.film_or_detector_model 'KODAK SO-163 FILM' _em_image_recording.imaging_id 1 _em_image_recording.detector_mode ? _em_image_recording.average_exposure_time ? _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.concentration 32 _em_specimen.vitrification_applied YES _em_specimen.staining_applied NO _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.details ? # _pdbx_coordinate_model.asym_id A _pdbx_coordinate_model.type 'P ATOMS ONLY' # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1OB2 # _atom_sites.entry_id 1QZB _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_type.symbol P # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 P P . C A 1 2 ? -5.758 0.226 -37.611 1.00 36.15 ? 2 C B P 1 ATOM 2 P P . G A 1 3 ? -7.548 -4.817 -35.780 1.00 38.57 ? 3 G B P 1 ATOM 3 P P . G A 1 4 ? -11.932 -7.551 -32.336 1.00 50.13 ? 4 G B P 1 ATOM 4 P P . A A 1 5 ? -16.795 -7.912 -28.958 1.00 46.12 ? 5 A B P 1 ATOM 5 P P . U A 1 6 ? -21.805 -6.611 -26.755 1.00 41.93 ? 6 U B P 1 ATOM 6 P P . U A 1 7 ? -26.975 -3.593 -26.744 1.00 39.61 ? 7 U B P 1 ATOM 7 P P . U A 1 8 ? -31.089 2.030 -27.580 1.00 38.44 ? 8 U B P 1 ATOM 8 P P . A A 1 9 ? -35.423 2.775 -28.335 1.00 30.30 ? 9 A B P 1 ATOM 9 P P . G A 1 10 ? -39.050 8.345 -28.654 1.00 36.63 ? 10 G B P 1 ATOM 10 P P . C A 1 11 ? -34.755 8.904 -24.262 1.00 48.28 ? 11 C B P 1 ATOM 11 P P . U A 1 12 ? -32.369 6.465 -19.720 1.00 38.23 ? 12 U B P 1 ATOM 12 P P . C A 1 13 ? -31.272 1.173 -17.685 1.00 37.44 ? 13 C B P 1 ATOM 13 P P . A A 1 14 ? -31.981 -5.471 -20.177 1.00 33.32 ? 14 A B P 1 ATOM 14 P P . G A 1 15 ? -33.645 -10.686 -23.328 1.00 33.55 ? 15 G B P 1 ATOM 15 P P . U A 1 16 ? -34.340 -13.695 -27.700 1.00 58.67 ? 16 U B P 1 ATOM 16 P P . U A 1 17 ? -33.883 -16.686 -32.752 1.00 63.01 ? 17 U B P 1 ATOM 17 P P . G A 1 18 ? -31.259 -15.909 -38.418 1.00 51.43 ? 18 G B P 1 ATOM 18 P P . G A 1 19 ? -37.225 -13.180 -38.500 1.00 56.66 ? 19 G B P 1 ATOM 19 P P . G A 1 20 ? -43.864 -11.829 -38.957 1.00 82.09 ? 20 G B P 1 ATOM 20 P P . A A 1 21 ? -43.635 -6.120 -36.923 1.00 46.40 ? 21 A B P 1 ATOM 21 P P . G A 1 22 ? -46.276 -4.974 -30.765 1.00 19.04 ? 22 G B P 1 ATOM 22 P P . A A 1 23 ? -47.138 -2.794 -24.117 1.00 28.32 ? 23 A B P 1 ATOM 23 P P . G A 1 24 ? -48.093 -1.758 -18.840 1.00 33.68 ? 24 G B P 1 ATOM 24 P P . C A 1 25 ? -47.497 2.456 -15.297 1.00 50.66 ? 25 C B P 1 ATOM 25 P P . G A 1 26 ? -46.529 8.123 -14.354 1.00 60.43 ? 26 G B P 1 ATOM 26 P P . C A 1 27 ? -46.631 13.381 -17.559 1.00 88.39 ? 27 C B P 1 ATOM 27 P P . C A 1 28 ? -50.041 15.583 -21.816 1.00 108.26 ? 28 C B P 1 ATOM 28 P P . A A 1 29 ? -55.442 16.471 -23.178 1.00 132.50 ? 29 A B P 1 ATOM 29 P P . G A 1 30 ? -61.462 15.138 -21.832 1.00 164.78 ? 30 G B P 1 ATOM 30 P P . A A 1 31 ? -66.694 12.686 -19.173 1.00 172.07 ? 31 A B P 1 ATOM 31 P P . C A 1 32 ? -67.465 12.084 -14.147 1.00 176.80 ? 32 C B P 1 ATOM 32 P P . U A 1 33 ? -68.159 13.437 -8.953 1.00 200.00 ? 33 U B P 1 ATOM 33 P P . G A 1 34 ? -67.519 18.178 -6.035 1.00 193.77 ? 34 G B P 1 ATOM 34 P P . A A 1 35 ? -64.029 19.550 -9.947 1.00 185.75 ? 35 A B P 1 ATOM 35 P P . A A 1 36 ? -57.782 18.089 -10.796 1.00 196.33 ? 36 A B P 1 ATOM 36 P P . G A 1 37 ? -52.701 16.655 -10.766 1.00 200.00 ? 37 G B P 1 ATOM 37 P P . A A 1 38 ? -50.476 11.124 -9.444 1.00 193.90 ? 38 A B P 1 ATOM 38 P P . U A 1 39 ? -50.948 5.622 -8.416 1.00 171.33 ? 39 U B P 1 ATOM 39 P P . C A 1 40 ? -54.795 1.745 -11.425 1.00 160.10 ? 40 C B P 1 ATOM 40 P P . U A 1 41 ? -58.057 -0.588 -15.208 1.00 138.03 ? 41 U B P 1 ATOM 41 P P . G A 1 42 ? -59.186 -0.594 -20.774 1.00 119.52 ? 42 G B P 1 ATOM 42 P P . G A 1 43 ? -57.754 1.195 -26.794 1.00 93.55 ? 43 G B P 1 ATOM 43 P P . A A 1 44 ? -53.639 3.584 -31.333 1.00 91.74 ? 44 A B P 1 ATOM 44 P P . G A 1 45 ? -49.295 5.893 -33.760 1.00 78.71 ? 45 G B P 1 ATOM 45 P P . G A 1 46 ? -43.788 6.888 -33.961 1.00 60.98 ? 46 G B P 1 ATOM 46 P P . U A 1 47 ? -37.838 6.244 -35.147 1.00 78.20 ? 47 U B P 1 ATOM 47 P P . C A 1 48 ? -35.552 0.173 -37.919 1.00 52.65 ? 48 C B P 1 ATOM 48 P P . C A 1 49 ? -30.710 -0.642 -33.151 1.00 17.11 ? 49 C B P 1 ATOM 49 P P . U A 1 50 ? -31.003 2.711 -37.547 1.00 17.58 ? 50 U B P 1 ATOM 50 P P . G A 1 51 ? -30.216 3.602 -43.159 1.00 21.85 ? 51 G B P 1 ATOM 51 P P . U A 1 52 ? -28.755 2.168 -48.651 1.00 7.73 ? 52 U B P 1 ATOM 52 P P . G A 1 53 ? -27.240 -2.779 -52.407 1.00 11.78 ? 53 G B P 1 ATOM 53 P P . U A 1 54 ? -26.502 -8.282 -54.350 1.00 17.41 ? 54 U B P 1 ATOM 54 P P . U A 1 55 ? -28.779 -13.145 -54.296 1.00 30.57 ? 55 U B P 1 ATOM 55 P P . C A 1 56 ? -33.926 -14.897 -54.061 1.00 40.60 ? 56 C B P 1 ATOM 56 P P . G A 1 57 ? -35.724 -10.053 -52.490 1.00 37.48 ? 57 G B P 1 ATOM 57 P P . A A 1 58 ? -35.429 -6.974 -47.533 1.00 32.55 ? 58 A B P 1 ATOM 58 P P . U A 1 59 ? -34.995 -4.688 -41.776 1.00 48.23 ? 59 U B P 1 ATOM 59 P P . C A 1 60 ? -30.358 -6.402 -39.602 1.00 26.95 ? 60 C B P 1 ATOM 60 P P . C A 1 61 ? -25.991 -10.032 -36.513 1.00 28.80 ? 61 C B P 1 ATOM 61 P P . A A 1 62 ? -21.743 -11.751 -39.587 1.00 25.23 ? 62 A B P 1 ATOM 62 P P . C A 1 63 ? -17.611 -9.879 -42.987 1.00 28.44 ? 63 C B P 1 ATOM 63 P P . A A 1 64 ? -14.912 -4.910 -45.463 1.00 30.74 ? 64 A B P 1 ATOM 64 P P . G A 1 65 ? -14.792 1.623 -43.525 1.00 13.07 ? 65 G B P 1 ATOM 65 P P . A A 1 66 ? -16.376 5.987 -38.708 1.00 22.92 ? 66 A B P 1 ATOM 66 P P . A A 1 67 ? -18.028 9.316 -34.410 1.00 22.81 ? 67 A B P 1 ATOM 67 P P . U A 1 68 ? -18.743 10.679 -28.875 1.00 45.82 ? 68 U B P 1 ATOM 68 P P . U A 1 69 ? -17.308 8.873 -23.402 1.00 51.04 ? 69 U B P 1 ATOM 69 P P . C A 1 70 ? -13.801 4.791 -20.033 1.00 50.83 ? 70 C B P 1 ATOM 70 P P . G A 1 71 ? -9.372 1.245 -18.842 1.00 54.67 ? 71 G B P 1 ATOM 71 P P . C A 1 72 ? -3.810 -1.314 -20.206 1.00 59.46 ? 72 C B P 1 ATOM 72 P P . A A 1 73 ? 0.567 -1.911 -22.800 1.00 59.61 ? 73 A B P 1 ATOM 73 P P . C A 1 74 ? 4.732 -2.057 -20.714 1.00 59.61 ? 74 C B P 1 ATOM 74 P P . C A 1 75 ? 9.331 -7.269 -18.282 1.00 55.58 ? 75 C B P 1 ATOM 75 P P . A A 1 76 ? 14.175 -6.671 -16.870 1.00 59.61 ? 76 A B P 1 #