data_1QZA
#
_entry.id 1QZA
#
_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 1QZA pdb_00001qza 10.2210/pdb1qza/pdb
RCSB RCSB020251 ? ?
WWPDB D_1000020251 ? ?
#
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 1QZA
_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 1QZB 'Coordinates of the A-site tRNA model fitted into the cryo-EM map of 70S ribosome in the pre-translocational state'
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-1055 . '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 24189.365
_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 GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACC
_entity_poly.pdbx_seq_one_letter_code_can GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACC
_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
#
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 1 G G 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
#
_cell.entry_id 1QZA
_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 1QZA
_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 1QZA
_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 1QZA
_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 1QZA
_struct.title
'Coordinates of the A/T site tRNA model fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 1QZA
_struct_keywords.pdbx_keywords RNA
_struct_keywords.text 'tRNA model, decoding, A/T-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 1QZA
_struct_ref.pdbx_db_accession 1QZA
_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 1QZA
_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 75
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession 1QZA
_struct_ref_seq.db_align_beg 1
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 75
_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 75
#
_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 1QZA
_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 1QZA
_em_3d_reconstruction.id 1
_em_3d_reconstruction.symmetry_type POINT
_em_3d_reconstruction.num_particles 75996
_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 10
_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 + fMet-tRNA + PhetRNA + EF-Tu + GDP + kir mRNA codes for MP-stop' ?
2 tRNA ? 1 ? ? ?
#
_em_imaging.entry_id 1QZA
_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 ?
_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 1QZA
_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 1QZA
_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 1QZA
_em_single_particle_entity.id 1
_em_single_particle_entity.point_symmetry C1
_em_single_particle_entity.image_processing_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 1QZA
_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 . G A 1 1 ? -24.604 51.452 -47.785 1.00 37.10 ? 1 G B P 1
ATOM 2 P P . C A 1 2 ? -22.560 47.565 -50.981 1.00 0.00 ? 2 C B P 1
ATOM 3 P P . G A 1 3 ? -19.739 42.120 -50.271 1.00 0.00 ? 3 G B P 1
ATOM 4 P P . G A 1 4 ? -19.552 36.440 -46.055 1.00 0.00 ? 4 G B P 1
ATOM 5 P P . A A 1 5 ? -21.173 32.188 -41.018 1.00 0.00 ? 5 A B P 1
ATOM 6 P P . U A 1 6 ? -24.381 29.372 -36.707 1.00 0.00 ? 6 U B P 1
ATOM 7 P P . U A 1 7 ? -29.927 27.806 -34.668 1.00 0.00 ? 7 U B P 1
ATOM 8 P P . U A 1 8 ? -36.011 27.557 -33.938 1.00 0.00 ? 8 U B P 1
ATOM 9 P P . A A 1 9 ? -39.932 25.127 -32.665 1.00 0.00 ? 9 A B P 1
ATOM 10 P P . G A 1 10 ? -45.490 23.645 -32.338 1.00 0.00 ? 10 G B P 1
ATOM 11 P P . C A 1 11 ? -42.126 27.657 -29.337 1.00 0.00 ? 11 C B P 1
ATOM 12 P P . U A 1 12 ? -37.610 28.609 -25.970 1.00 0.00 ? 12 U B P 1
ATOM 13 P P . C A 1 13 ? -32.136 26.389 -24.891 1.00 0.00 ? 13 C B P 1
ATOM 14 P P . A A 1 14 ? -29.218 21.238 -28.901 1.00 0.00 ? 14 A B P 1
ATOM 15 P P . G A 1 15 ? -27.223 15.733 -31.578 1.00 0.00 ? 15 G B P 1
ATOM 16 P P . U A 1 16 ? -27.016 12.313 -36.378 1.00 0.00 ? 16 U B P 1
ATOM 17 P P . U A 1 17 ? -27.326 11.992 -42.221 1.00 0.00 ? 17 U B P 1
ATOM 18 P P . G A 1 18 ? -28.394 14.643 -46.927 1.00 0.00 ? 18 G B P 1
ATOM 19 P P . G A 1 19 ? -33.871 11.573 -44.790 1.00 0.00 ? 19 G B P 1
ATOM 20 P P . G A 1 20 ? -38.064 6.551 -44.178 1.00 0.00 ? 20 G B P 1
ATOM 21 P P . A A 1 21 ? -41.717 11.613 -41.541 1.00 0.00 ? 21 A B P 1
ATOM 22 P P . G A 1 22 ? -42.126 11.634 -34.331 1.00 0.00 ? 22 G B P 1
ATOM 23 P P . A A 1 23 ? -40.583 10.555 -27.786 1.00 0.00 ? 23 A B P 1
ATOM 24 P P . G A 1 24 ? -39.377 11.135 -22.148 1.00 0.00 ? 24 G B P 1
ATOM 25 P P . C A 1 25 ? -40.644 15.200 -17.716 1.00 0.00 ? 25 C B P 1
ATOM 26 P P . G A 1 26 ? -43.855 19.874 -15.996 1.00 0.00 ? 26 G B P 1
ATOM 27 P P . C A 1 27 ? -49.311 22.625 -17.327 1.00 0.00 ? 27 C B P 1
ATOM 28 P P . C A 1 28 ? -53.882 21.353 -21.036 1.00 0.00 ? 28 C B P 1
ATOM 29 P P . A A 1 29 ? -58.838 19.067 -23.494 1.00 0.00 ? 29 A B P 1
ATOM 30 P P . G A 1 30 ? -63.013 14.641 -22.119 1.00 0.00 ? 30 G B P 1
ATOM 31 P P . A A 1 31 ? -66.043 10.988 -18.336 1.00 0.00 ? 31 A B P 1
ATOM 32 P P . C A 1 32 ? -66.924 10.799 -14.263 1.00 0.00 ? 32 C B P 1
ATOM 33 P P . U A 1 33 ? -67.867 13.863 -8.776 1.00 0.00 ? 33 U B P 1
ATOM 34 P P . G A 1 34 ? -67.177 17.903 -6.064 1.00 0.00 ? 34 G B P 1
ATOM 35 P P . A A 1 35 ? -63.937 19.519 -10.485 1.00 0.00 ? 35 A B P 1
ATOM 36 P P . A A 1 36 ? -57.948 19.157 -11.951 1.00 0.00 ? 36 A B P 1
ATOM 37 P P . G A 1 37 ? -52.379 16.963 -10.622 1.00 0.00 ? 37 G B P 1
ATOM 38 P P . A A 1 38 ? -49.474 12.375 -7.984 1.00 0.00 ? 38 A B P 1
ATOM 39 P P . U A 1 39 ? -50.202 6.736 -7.874 1.00 0.00 ? 39 U B P 1
ATOM 40 P P . C A 1 40 ? -52.368 3.128 -11.870 1.00 0.00 ? 40 C B P 1
ATOM 41 P P . U A 1 41 ? -54.242 1.488 -16.381 1.00 0.00 ? 41 U B P 1
ATOM 42 P P . G A 1 42 ? -53.534 1.814 -21.904 1.00 0.00 ? 42 G B P 1
ATOM 43 P P . G A 1 43 ? -52.210 4.503 -27.390 1.00 0.00 ? 43 G B P 1
ATOM 44 P P . A A 1 44 ? -51.312 10.611 -30.869 1.00 0.00 ? 44 A B P 1
ATOM 45 P P . G A 1 45 ? -51.605 15.468 -32.986 1.00 0.00 ? 45 G B P 1
ATOM 46 P P . G A 1 46 ? -48.719 18.715 -35.203 1.00 0.00 ? 46 G B P 1
ATOM 47 P P . U A 1 47 ? -45.894 23.684 -37.084 1.00 0.00 ? 47 U B P 1
ATOM 48 P P . C A 1 48 ? -41.348 22.647 -42.021 1.00 0.00 ? 48 C B P 1
ATOM 49 P P . C A 1 49 ? -35.673 25.880 -39.819 1.00 0.00 ? 49 C B P 1
ATOM 50 P P . U A 1 50 ? -40.688 27.567 -42.595 1.00 0.00 ? 50 U B P 1
ATOM 51 P P . G A 1 51 ? -43.258 29.571 -47.495 1.00 0.00 ? 51 G B P 1
ATOM 52 P P . U A 1 52 ? -43.475 29.778 -53.229 1.00 0.00 ? 52 U B P 1
ATOM 53 P P . G A 1 53 ? -40.169 26.186 -58.189 1.00 0.00 ? 53 G B P 1
ATOM 54 P P . U A 1 54 ? -36.416 22.686 -61.345 1.00 0.00 ? 54 U B P 1
ATOM 55 P P . U A 1 55 ? -34.002 17.671 -62.012 1.00 0.00 ? 55 U B P 1
ATOM 56 P P . C A 1 56 ? -35.642 12.615 -61.499 1.00 0.00 ? 56 C B P 1
ATOM 57 P P . G A 1 57 ? -39.689 13.906 -57.695 1.00 0.00 ? 57 G B P 1
ATOM 58 P P . A A 1 58 ? -40.338 15.684 -52.607 1.00 0.00 ? 58 A B P 1
ATOM 59 P P . U A 1 59 ? -39.405 18.075 -46.936 1.00 0.00 ? 59 U B P 1
ATOM 60 P P . C A 1 60 ? -34.663 20.553 -47.045 1.00 0.00 ? 60 C B P 1
ATOM 61 P P . C A 1 61 ? -28.255 21.924 -46.596 1.00 0.00 ? 61 C B P 1
ATOM 62 P P . A A 1 62 ? -26.057 23.937 -51.197 1.00 0.00 ? 62 A B P 1
ATOM 63 P P . C A 1 63 ? -26.114 28.249 -54.910 1.00 0.00 ? 63 C B P 1
ATOM 64 P P . A A 1 64 ? -28.534 33.923 -55.347 1.00 0.00 ? 64 A B P 1
ATOM 65 P P . G A 1 65 ? -32.342 39.392 -53.123 1.00 0.00 ? 65 G B P 1
ATOM 66 P P . A A 1 66 ? -35.304 42.378 -47.724 1.00 0.00 ? 66 A B P 1
ATOM 67 P P . A A 1 67 ? -36.429 43.872 -42.221 1.00 0.00 ? 67 A B P 1
ATOM 68 P P . U A 1 68 ? -35.061 43.959 -36.052 1.00 0.00 ? 68 U B P 1
ATOM 69 P P . U A 1 69 ? -31.431 42.711 -31.457 1.00 0.00 ? 69 U B P 1
ATOM 70 P P . C A 1 70 ? -24.485 42.235 -30.365 1.00 0.00 ? 70 C B P 1
ATOM 71 P P . G A 1 71 ? -18.649 41.323 -31.441 1.00 0.00 ? 71 G B P 1
ATOM 72 P P . C A 1 72 ? -13.515 43.826 -35.551 1.00 0.00 ? 72 C B P 1
ATOM 73 P P . A A 1 73 ? -11.378 48.131 -40.556 1.00 0.00 ? 73 A B P 1
ATOM 74 P P . C A 1 74 ? -11.518 53.397 -44.780 1.00 0.00 ? 74 C B P 1
ATOM 75 P P . C A 1 75 ? -13.042 58.653 -46.853 1.00 0.00 ? 75 C B P 1
#