data_3P4C # _entry.id 3P4C # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3P4C pdb_00003p4c 10.2210/pdb3p4c/pdb NDB NA0811 ? ? RCSB RCSB061939 ? ? WWPDB D_1000061939 ? ? # 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 2011-01-05 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-08 4 'Structure model' 1 3 2020-06-24 5 'Structure model' 1 4 2024-02-21 # _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' 'Refinement description' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Source and taxonomy' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' 8 5 'Structure model' 'Derived calculations' # 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' software 2 4 'Structure model' pdbx_entity_src_syn 3 4 'Structure model' struct_conn 4 4 'Structure model' struct_ref 5 4 'Structure model' struct_ref_seq 6 5 'Structure model' chem_comp_atom 7 5 'Structure model' chem_comp_bond 8 5 'Structure model' database_2 9 5 'Structure model' struct_site # 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' '_software.name' 2 4 'Structure model' '_pdbx_entity_src_syn.ncbi_taxonomy_id' 3 4 'Structure model' '_pdbx_entity_src_syn.organism_scientific' 4 4 'Structure model' '_pdbx_entity_src_syn.pdbx_beg_seq_num' 5 4 'Structure model' '_pdbx_entity_src_syn.pdbx_end_seq_num' 6 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 5 'Structure model' '_database_2.pdbx_DOI' 8 5 'Structure model' '_database_2.pdbx_database_accession' 9 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 10 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 11 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3P4C _pdbx_database_status.recvd_initial_deposition_date 2010-10-06 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3P4B . unspecified PDB 3P4D . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pallan, P.S.' 1 'Greene, E.M.' 2 'Jicman, P.A.' 3 'Pandey, R.K.' 4 'Manoharan, M.' 5 'Rozners, E.' 6 'Egli, M.' 7 # _citation.id primary _citation.title ;Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 39 _citation.page_first 3482 _citation.page_last 3495 _citation.year 2011 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21183463 _citation.pdbx_database_id_DOI 10.1093/nar/gkq1270 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pallan, P.S.' 1 ? primary 'Greene, E.M.' 2 ? primary 'Jicman, P.A.' 3 ? primary 'Pandey, R.K.' 4 ? primary 'Manoharan, M.' 5 ? primary 'Rozners, E.' 6 ? primary 'Egli, M.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'" 2534.525 2 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 3 ? ? ? ? 3 water nat water 18.015 93 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(CFZ)G(AF2)A(UFT)U(CFZ)G' _entity_poly.pdbx_seq_one_letter_code_can XGXAUUXG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 CFZ n 1 2 G n 1 3 AF2 n 1 4 A n 1 5 UFT n 1 6 U n 1 7 CFZ n 1 8 G 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 8 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'Chemically synthesized modified RNA' # 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 AF2 'DNA linking' n ;2'-deoxy-2'-fluoroadenosine 5'-(dihydrogen phosphate) ; ? 'C10 H13 F N5 O6 P' 349.212 CFZ 'DNA linking' n ;2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate) ; ? 'C9 H13 F N3 O7 P' 325.188 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 UFT 'DNA linking' n ;2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate) ; ? 'C9 H12 F N2 O8 P' 326.172 # 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 CFZ 1 101 101 CFZ CFZ A . n A 1 2 G 2 102 102 G G A . n A 1 3 AF2 3 103 103 AF2 AF2 A . n A 1 4 A 4 104 104 A A A . n A 1 5 UFT 5 105 105 UFT UFT A . n A 1 6 U 6 106 106 U U A . n A 1 7 CFZ 7 107 107 CFZ CFZ A . n A 1 8 G 8 108 108 G G A . n B 1 1 CFZ 1 209 209 CFZ CFZ B . n B 1 2 G 2 210 210 G G B . n B 1 3 AF2 3 211 211 AF2 AF2 B . n B 1 4 A 4 212 212 A A B . n B 1 5 UFT 5 213 213 UFT UFT B . n B 1 6 U 6 214 214 U U B . n B 1 7 CFZ 7 215 215 CFZ CFZ B . n B 1 8 G 8 216 216 G G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SR 1 301 301 SR SR B . D 2 SR 1 302 302 SR SR B . E 2 SR 1 303 303 SR SR B . F 3 HOH 1 305 305 HOH HOH A . F 3 HOH 2 306 306 HOH HOH A . F 3 HOH 3 309 309 HOH HOH A . F 3 HOH 4 310 310 HOH HOH A . F 3 HOH 5 311 311 HOH HOH A . F 3 HOH 6 312 312 HOH HOH A . F 3 HOH 7 314 314 HOH HOH A . F 3 HOH 8 315 315 HOH HOH A . F 3 HOH 9 316 316 HOH HOH A . F 3 HOH 10 317 317 HOH HOH A . F 3 HOH 11 318 318 HOH HOH A . F 3 HOH 12 320 320 HOH HOH A . F 3 HOH 13 322 322 HOH HOH A . F 3 HOH 14 325 325 HOH HOH A . F 3 HOH 15 326 326 HOH HOH A . F 3 HOH 16 327 327 HOH HOH A . F 3 HOH 17 330 330 HOH HOH A . F 3 HOH 18 333 333 HOH HOH A . F 3 HOH 19 334 334 HOH HOH A . F 3 HOH 20 337 337 HOH HOH A . F 3 HOH 21 338 338 HOH HOH A . F 3 HOH 22 340 340 HOH HOH A . F 3 HOH 23 343 343 HOH HOH A . F 3 HOH 24 346 346 HOH HOH A . F 3 HOH 25 348 348 HOH HOH A . F 3 HOH 26 349 349 HOH HOH A . F 3 HOH 27 354 354 HOH HOH A . F 3 HOH 28 355 355 HOH HOH A . F 3 HOH 29 356 356 HOH HOH A . F 3 HOH 30 360 360 HOH HOH A . F 3 HOH 31 362 362 HOH HOH A . F 3 HOH 32 363 363 HOH HOH A . F 3 HOH 33 364 364 HOH HOH A . F 3 HOH 34 366 366 HOH HOH A . F 3 HOH 35 370 370 HOH HOH A . F 3 HOH 36 371 371 HOH HOH A . F 3 HOH 37 372 372 HOH HOH A . F 3 HOH 38 374 374 HOH HOH A . F 3 HOH 39 379 379 HOH HOH A . F 3 HOH 40 380 380 HOH HOH A . F 3 HOH 41 381 381 HOH HOH A . F 3 HOH 42 382 382 HOH HOH A . F 3 HOH 43 387 387 HOH HOH A . F 3 HOH 44 391 391 HOH HOH A . F 3 HOH 45 395 395 HOH HOH A . G 3 HOH 1 304 304 HOH HOH B . G 3 HOH 2 307 307 HOH HOH B . G 3 HOH 3 308 308 HOH HOH B . G 3 HOH 4 313 313 HOH HOH B . G 3 HOH 5 319 319 HOH HOH B . G 3 HOH 6 321 321 HOH HOH B . G 3 HOH 7 323 323 HOH HOH B . G 3 HOH 8 324 324 HOH HOH B . G 3 HOH 9 328 328 HOH HOH B . G 3 HOH 10 329 329 HOH HOH B . G 3 HOH 11 331 331 HOH HOH B . G 3 HOH 12 332 332 HOH HOH B . G 3 HOH 13 335 335 HOH HOH B . G 3 HOH 14 336 336 HOH HOH B . G 3 HOH 15 339 339 HOH HOH B . G 3 HOH 16 341 341 HOH HOH B . G 3 HOH 17 342 342 HOH HOH B . G 3 HOH 18 344 344 HOH HOH B . G 3 HOH 19 345 345 HOH HOH B . G 3 HOH 20 347 347 HOH HOH B . G 3 HOH 21 350 350 HOH HOH B . G 3 HOH 22 351 351 HOH HOH B . G 3 HOH 23 352 352 HOH HOH B . G 3 HOH 24 353 353 HOH HOH B . G 3 HOH 25 357 357 HOH HOH B . G 3 HOH 26 358 358 HOH HOH B . G 3 HOH 27 359 359 HOH HOH B . G 3 HOH 28 361 361 HOH HOH B . G 3 HOH 29 365 365 HOH HOH B . G 3 HOH 30 367 367 HOH HOH B . G 3 HOH 31 368 368 HOH HOH B . G 3 HOH 32 369 369 HOH HOH B . G 3 HOH 33 373 373 HOH HOH B . G 3 HOH 34 375 375 HOH HOH B . G 3 HOH 35 376 376 HOH HOH B . G 3 HOH 36 377 377 HOH HOH B . G 3 HOH 37 378 378 HOH HOH B . G 3 HOH 38 383 383 HOH HOH B . G 3 HOH 39 384 384 HOH HOH B . G 3 HOH 40 385 385 HOH HOH B . G 3 HOH 41 386 386 HOH HOH B . G 3 HOH 42 388 388 HOH HOH B . G 3 HOH 43 389 389 HOH HOH B . G 3 HOH 44 390 390 HOH HOH B . G 3 HOH 45 392 392 HOH HOH B . G 3 HOH 46 393 393 HOH HOH B . G 3 HOH 47 394 394 HOH HOH B . G 3 HOH 48 396 396 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 HKL2Map 'model building' . ? 2 SHELXL refinement . ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 HKL2Map phasing . ? 6 SHELXL-97 refinement . ? 7 # _cell.entry_id 3P4C _cell.length_a 40.550 _cell.length_b 40.550 _cell.length_c 117.222 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? _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 3P4C _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3P4C _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.83 _exptl_crystal.density_percent_sol 32.77 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;Sodium cacodylate (40 mM, pH 6.0), lithium chloride (40 mM), strontium chloride (80 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated against a reservoir of MPD (1 mL, 35%) , VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.pdbx_collection_date 2008-11-16 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol SAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.7687 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 21-ID-D' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 21-ID-D _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.7687 # _reflns.entry_id 3P4C _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.0 _reflns.d_resolution_high 1.15 _reflns.number_obs 13343 _reflns.number_all 13629 _reflns.percent_possible_obs 97.9 _reflns.pdbx_Rmerge_I_obs 0.095 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 50.1 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 15.1 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.15 _reflns_shell.d_res_low 1.17 _reflns_shell.percent_possible_all 72.9 _reflns_shell.Rmerge_I_obs 0.408 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.43 _reflns_shell.pdbx_redundancy 3.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 489 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3P4C _refine.ls_number_reflns_obs 13314 _refine.ls_number_reflns_all 13343 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 50 _refine.ls_d_res_high 1.15 _refine.ls_percent_reflns_obs 99.8 _refine.ls_R_factor_obs 0.182 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.182 _refine.ls_R_factor_R_free 0.249 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 666 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work 0.182 _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 334 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 93 _refine_hist.number_atoms_total 430 _refine_hist.d_res_high 1.15 _refine_hist.d_res_low 50 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.01 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.027 ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 3P4C _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 3P4C _struct.title ;Alternatingly modified 2'Fluoro RNA octamer f/rA2U2-R32 ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3P4C _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;RNA, 2'-FLUORO-RNA O2'-MODIFICATION, OCTAMER, 2'-fluoro 2'-deoxycytidine, 2'-fluoro 2'-deoxyadenosine, 2'-fluoro 2'-deoxyuridine, siRNA ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 3 ? G N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3P4C _struct_ref.pdbx_db_accession 3P4C _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3P4C A 1 ? 8 ? 3P4C 101 ? 108 ? 101 108 2 1 3P4C B 1 ? 8 ? 3P4C 209 ? 216 ? 209 216 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 software_defined_assembly PISA tetrameric 4 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 2 'ABSA (A^2)' 3920 ? 2 MORE -146 ? 2 'SSA (A^2)' 4780 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D,E,F,G 2 1,2 A,B,C,D,E,F,G # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 17_555 x-y+1/3,-y+2/3,-z+2/3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 23.4115534156 0.0000000000 0.0000000000 -1.0000000000 78.1480000000 # _struct_biol.id 1 _struct_biol.details ? # 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 covale1 covale both ? A CFZ 1 "O3'" ? ? ? 1_555 A G 2 P ? ? A CFZ 101 A G 102 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale2 covale both ? A G 2 "O3'" ? ? ? 1_555 A AF2 3 P ? ? A G 102 A AF2 103 1_555 ? ? ? ? ? ? ? 1.588 ? ? covale3 covale one ? A AF2 3 "O3'" ? ? ? 1_555 A A 4 P ? ? A AF2 103 A A 104 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale4 covale both ? A A 4 "O3'" ? ? ? 1_555 A UFT 5 P ? ? A A 104 A UFT 105 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale5 covale both ? A UFT 5 "O3'" ? ? ? 1_555 A U 6 P ? ? A UFT 105 A U 106 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale6 covale both ? A U 6 "O3'" ? ? ? 1_555 A CFZ 7 P ? ? A U 106 A CFZ 107 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale7 covale both ? A CFZ 7 "O3'" ? ? ? 1_555 A G 8 P ? ? A CFZ 107 A G 108 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale8 covale both ? B CFZ 1 "O3'" ? ? ? 1_555 B G 2 P ? ? B CFZ 209 B G 210 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale9 covale both ? B G 2 "O3'" ? ? ? 1_555 B AF2 3 P ? ? B G 210 B AF2 211 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale10 covale one ? B AF2 3 "O3'" ? ? ? 1_555 B A 4 P ? ? B AF2 211 B A 212 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale11 covale both ? B A 4 "O3'" ? ? ? 1_555 B UFT 5 P ? ? B A 212 B UFT 213 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale12 covale both ? B UFT 5 "O3'" ? ? ? 1_555 B U 6 P ? ? B UFT 213 B U 214 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale13 covale both ? B U 6 "O3'" ? ? ? 1_555 B CFZ 7 P ? ? B U 214 B CFZ 215 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale14 covale both ? B CFZ 7 "O3'" ? ? ? 1_555 B G 8 P ? ? B CFZ 215 B G 216 1_555 ? ? ? ? ? ? ? 1.599 ? ? hydrog1 hydrog ? ? A A 4 N1 ? ? ? 1_555 B UFT 5 N3 ? ? A A 104 B UFT 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 4 N6 ? ? ? 1_555 B UFT 5 O4 ? ? A A 104 B UFT 213 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A UFT 5 N3 ? ? ? 1_555 B A 4 N1 ? ? A UFT 105 B A 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A UFT 5 O4 ? ? ? 1_555 B A 4 N6 ? ? A UFT 105 B A 212 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B SR 301 ? 5 'BINDING SITE FOR RESIDUE SR B 301' AC2 Software B SR 302 ? 9 'BINDING SITE FOR RESIDUE SR B 302' AC3 Software B SR 303 ? 3 'BINDING SITE FOR RESIDUE SR B 303' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 G A 8 ? G A 108 . ? 17_555 ? 2 AC1 5 HOH F . ? HOH A 330 . ? 17_555 ? 3 AC1 5 HOH F . ? HOH A 371 . ? 17_555 ? 4 AC1 5 CFZ B 1 ? CFZ B 209 . ? 1_555 ? 5 AC1 5 G B 2 ? G B 210 . ? 1_555 ? 6 AC2 9 HOH F . ? HOH A 310 . ? 1_555 ? 7 AC2 9 HOH F . ? HOH A 334 . ? 1_555 ? 8 AC2 9 HOH F . ? HOH A 355 . ? 1_555 ? 9 AC2 9 HOH F . ? HOH A 372 . ? 1_555 ? 10 AC2 9 UFT B 5 ? UFT B 213 . ? 1_555 ? 11 AC2 9 HOH G . ? HOH B 308 . ? 1_555 ? 12 AC2 9 HOH G . ? HOH B 336 . ? 1_555 ? 13 AC2 9 HOH G . ? HOH B 352 . ? 1_555 ? 14 AC2 9 HOH G . ? HOH B 375 . ? 1_555 ? 15 AC3 3 HOH G . ? HOH B 378 . ? 3_555 ? 16 AC3 3 HOH G . ? HOH B 378 . ? 1_555 ? 17 AC3 3 HOH G . ? HOH B 378 . ? 2_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C2'" A A 104 ? ? "O2'" A A 104 ? ? 1.309 1.412 -0.103 0.013 N 2 1 "C2'" A U 106 ? ? "O2'" A U 106 ? ? 1.517 1.420 0.097 0.010 N 3 1 "C2'" A G 108 ? A "O2'" A G 108 ? A 1.484 1.420 0.064 0.010 N 4 1 "C2'" A G 108 ? B "O2'" A G 108 ? B 1.671 1.420 0.251 0.010 N 5 1 "C2'" B G 210 ? ? "O2'" B G 210 ? ? 1.510 1.420 0.090 0.010 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N1 A A 104 ? ? C2 A A 104 ? ? N3 A A 104 ? ? 125.96 129.30 -3.34 0.50 N 2 1 "O5'" A G 108 ? A "C5'" A G 108 ? A "C4'" A G 108 ? A 103.89 109.40 -5.51 0.80 N 3 1 "O5'" A G 108 ? B "C5'" A G 108 ? B "C4'" A G 108 ? B 102.54 109.40 -6.86 0.80 N 4 1 C6 A G 108 ? B N1 A G 108 ? B C2 A G 108 ? B 130.28 125.10 5.18 0.60 N 5 1 C2 A G 108 ? B N3 A G 108 ? B C4 A G 108 ? B 108.73 111.90 -3.17 0.50 N 6 1 N3 A G 108 ? A C4 A G 108 ? A C5 A G 108 ? A 124.87 128.60 -3.73 0.50 N 7 1 N3 A G 108 ? B C4 A G 108 ? B C5 A G 108 ? B 133.83 128.60 5.23 0.50 N 8 1 C5 A G 108 ? B C6 A G 108 ? B N1 A G 108 ? B 108.43 111.50 -3.07 0.50 N 9 1 N3 A G 108 ? A C4 A G 108 ? A N9 A G 108 ? A 130.52 126.00 4.52 0.60 N 10 1 N3 A G 108 ? B C4 A G 108 ? B N9 A G 108 ? B 119.34 126.00 -6.66 0.60 N 11 1 N1 A G 108 ? B C2 A G 108 ? B N2 A G 108 ? B 121.73 116.20 5.53 0.90 N 12 1 N1 A G 108 ? B C6 A G 108 ? B O6 A G 108 ? B 123.61 119.90 3.71 0.60 N 13 1 C5 A G 108 ? A C6 A G 108 ? A O6 A G 108 ? A 123.70 128.60 -4.90 0.60 N 14 1 N1 B A 212 ? ? C2 B A 212 ? ? N3 B A 212 ? ? 132.43 129.30 3.13 0.50 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A CFZ 1 A CFZ 101 ? DC ? 2 A AF2 3 A AF2 103 ? DA ? 3 A UFT 5 A UFT 105 ? DU ? 4 A CFZ 7 A CFZ 107 ? DC ? 5 B CFZ 1 B CFZ 209 ? DC ? 6 B AF2 3 B AF2 211 ? DA ? 7 B UFT 5 B UFT 213 ? DU ? 8 B CFZ 7 B CFZ 215 ? DC ? # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 B SR 303 ? E SR . 2 1 A HOH 322 ? F HOH . 3 1 A HOH 343 ? F HOH . 4 1 A HOH 363 ? F HOH . 5 1 A HOH 387 ? F HOH . 6 1 B HOH 328 ? G HOH . 7 1 B HOH 392 ? G HOH . # 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 AF2 F F N N 38 AF2 P P N N 39 AF2 N1 N Y N 40 AF2 C2 C Y N 41 AF2 N3 N Y N 42 AF2 C4 C Y N 43 AF2 C5 C Y N 44 AF2 C6 C Y N 45 AF2 N6 N N N 46 AF2 N7 N Y N 47 AF2 C8 C Y N 48 AF2 N9 N Y N 49 AF2 "C1'" C N R 50 AF2 OP2 O N N 51 AF2 "C2'" C N R 52 AF2 OP1 O N N 53 AF2 "C3'" C N R 54 AF2 "O3'" O N N 55 AF2 "C4'" C N R 56 AF2 "O4'" O N N 57 AF2 "C5'" C N N 58 AF2 "O5'" O N N 59 AF2 H2 H N N 60 AF2 H8 H N N 61 AF2 "H5'" H N N 62 AF2 "H5'A" H N N 63 AF2 "H1'" H N N 64 AF2 "H2'" H N N 65 AF2 "H3'" H N N 66 AF2 "H4'" H N N 67 AF2 HN6 H N N 68 AF2 HN6A H N N 69 AF2 HOP2 H N N 70 AF2 "HO3'" H N N 71 AF2 OP3 O N N 72 AF2 HOP3 H N N 73 CFZ P P N N 74 CFZ N1 N N N 75 CFZ C2 C N N 76 CFZ O2 O N N 77 CFZ N3 N N N 78 CFZ C4 C N N 79 CFZ N4 N N N 80 CFZ C5 C N N 81 CFZ C6 C N N 82 CFZ "C1'" C N R 83 CFZ O1P O N N 84 CFZ "C2'" C N R 85 CFZ "F2'" F N N 86 CFZ O2P O N N 87 CFZ "C3'" C N R 88 CFZ "O3'" O N N 89 CFZ O3P O N N 90 CFZ "C4'" C N R 91 CFZ "O4'" O N N 92 CFZ "C5'" C N N 93 CFZ "O5'" O N N 94 CFZ HN4 H N N 95 CFZ HN4A H N N 96 CFZ H5 H N N 97 CFZ H6 H N N 98 CFZ "H1'" H N N 99 CFZ HO1P H N N 100 CFZ "H2'" H N N 101 CFZ "H3'" H N N 102 CFZ "HO3'" H N N 103 CFZ HO3P H N N 104 CFZ "H4'" H N N 105 CFZ "H5'" H N N 106 CFZ "H5'A" H N N 107 G OP3 O N N 108 G P P N N 109 G OP1 O N N 110 G OP2 O N N 111 G "O5'" O N N 112 G "C5'" C N N 113 G "C4'" C N R 114 G "O4'" O N N 115 G "C3'" C N S 116 G "O3'" O N N 117 G "C2'" C N R 118 G "O2'" O N N 119 G "C1'" C N R 120 G N9 N Y N 121 G C8 C Y N 122 G N7 N Y N 123 G C5 C Y N 124 G C6 C N N 125 G O6 O N N 126 G N1 N N N 127 G C2 C N N 128 G N2 N N N 129 G N3 N N N 130 G C4 C Y N 131 G HOP3 H N N 132 G HOP2 H N N 133 G "H5'" H N N 134 G "H5''" H N N 135 G "H4'" H N N 136 G "H3'" H N N 137 G "HO3'" H N N 138 G "H2'" H N N 139 G "HO2'" H N N 140 G "H1'" H N N 141 G H8 H N N 142 G H1 H N N 143 G H21 H N N 144 G H22 H N N 145 HOH O O N N 146 HOH H1 H N N 147 HOH H2 H N N 148 SR SR SR N N 149 U OP3 O N N 150 U P P N N 151 U OP1 O N N 152 U OP2 O N N 153 U "O5'" O N N 154 U "C5'" C N N 155 U "C4'" C N R 156 U "O4'" O N N 157 U "C3'" C N S 158 U "O3'" O N N 159 U "C2'" C N R 160 U "O2'" O N N 161 U "C1'" C N R 162 U N1 N N N 163 U C2 C N N 164 U O2 O N N 165 U N3 N N N 166 U C4 C N N 167 U O4 O N N 168 U C5 C N N 169 U C6 C N N 170 U HOP3 H N N 171 U HOP2 H N N 172 U "H5'" H N N 173 U "H5''" H N N 174 U "H4'" H N N 175 U "H3'" H N N 176 U "HO3'" H N N 177 U "H2'" H N N 178 U "HO2'" H N N 179 U "H1'" H N N 180 U H3 H N N 181 U H5 H N N 182 U H6 H N N 183 UFT OP3 O N N 184 UFT P P N N 185 UFT OP1 O N N 186 UFT OP2 O N N 187 UFT "O5'" O N N 188 UFT N1 N N N 189 UFT C6 C N N 190 UFT C2 C N N 191 UFT O2 O N N 192 UFT N3 N N N 193 UFT C4 C N N 194 UFT O4 O N N 195 UFT C5 C N N 196 UFT "F2'" F N N 197 UFT "C2'" C N R 198 UFT "C5'" C N N 199 UFT "C4'" C N R 200 UFT "O4'" O N N 201 UFT "C1'" C N R 202 UFT "C3'" C N R 203 UFT "O3'" O N N 204 UFT HOP3 H N N 205 UFT HOP2 H N N 206 UFT H6 H N N 207 UFT H5 H N N 208 UFT "H2'" H N N 209 UFT "H5'" H N N 210 UFT "H5'A" H N N 211 UFT "H4'" H N N 212 UFT "H1'" H N N 213 UFT "H3'" H N N 214 UFT "HO3'" H N N 215 UFT HN3 H N N 216 # 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 AF2 F "C2'" sing N N 40 AF2 P OP1 doub N N 41 AF2 P OP2 sing N N 42 AF2 N1 C6 sing Y N 43 AF2 C2 N1 doub Y N 44 AF2 C2 N3 sing Y N 45 AF2 N3 C4 doub Y N 46 AF2 C4 N9 sing Y N 47 AF2 C4 C5 sing Y N 48 AF2 C5 N7 sing Y N 49 AF2 C6 C5 doub Y N 50 AF2 C6 N6 sing N N 51 AF2 N6 HN6A sing N N 52 AF2 C8 N7 doub Y N 53 AF2 C8 H8 sing N N 54 AF2 N9 C8 sing Y N 55 AF2 "C1'" N9 sing N N 56 AF2 "C1'" "C2'" sing N N 57 AF2 OP2 HOP2 sing N N 58 AF2 "C2'" "H2'" sing N N 59 AF2 "C2'" "C3'" sing N N 60 AF2 "C3'" "H3'" sing N N 61 AF2 "C3'" "O3'" sing N N 62 AF2 "O3'" "HO3'" sing N N 63 AF2 "C4'" "C3'" sing N N 64 AF2 "C4'" "C5'" sing N N 65 AF2 "O4'" "C1'" sing N N 66 AF2 "O4'" "C4'" sing N N 67 AF2 "C5'" "O5'" sing N N 68 AF2 "C5'" "H5'A" sing N N 69 AF2 "O5'" P sing N N 70 AF2 H2 C2 sing N N 71 AF2 "H5'" "C5'" sing N N 72 AF2 "H1'" "C1'" sing N N 73 AF2 "H4'" "C4'" sing N N 74 AF2 HN6 N6 sing N N 75 AF2 P OP3 sing N N 76 AF2 OP3 HOP3 sing N N 77 CFZ O2P P doub N N 78 CFZ P "O5'" sing N N 79 CFZ P O1P sing N N 80 CFZ P O3P sing N N 81 CFZ C6 N1 sing N N 82 CFZ C2 N1 sing N N 83 CFZ N1 "C1'" sing N N 84 CFZ N3 C2 sing N N 85 CFZ C2 O2 doub N N 86 CFZ C4 N3 doub N N 87 CFZ N4 C4 sing N N 88 CFZ C4 C5 sing N N 89 CFZ N4 HN4 sing N N 90 CFZ N4 HN4A sing N N 91 CFZ C5 C6 doub N N 92 CFZ C5 H5 sing N N 93 CFZ C6 H6 sing N N 94 CFZ "C2'" "C1'" sing N N 95 CFZ "C1'" "O4'" sing N N 96 CFZ "C1'" "H1'" sing N N 97 CFZ O1P HO1P sing N N 98 CFZ "C3'" "C2'" sing N N 99 CFZ "C2'" "F2'" sing N N 100 CFZ "C2'" "H2'" sing N N 101 CFZ "C3'" "O3'" sing N N 102 CFZ "C3'" "C4'" sing N N 103 CFZ "C3'" "H3'" sing N N 104 CFZ "O3'" "HO3'" sing N N 105 CFZ O3P HO3P sing N N 106 CFZ "O4'" "C4'" sing N N 107 CFZ "C5'" "C4'" sing N N 108 CFZ "C4'" "H4'" sing N N 109 CFZ "O5'" "C5'" sing N N 110 CFZ "C5'" "H5'" sing N N 111 CFZ "C5'" "H5'A" sing N N 112 G OP3 P sing N N 113 G OP3 HOP3 sing N N 114 G P OP1 doub N N 115 G P OP2 sing N N 116 G P "O5'" sing N N 117 G OP2 HOP2 sing N N 118 G "O5'" "C5'" sing N N 119 G "C5'" "C4'" sing N N 120 G "C5'" "H5'" sing N N 121 G "C5'" "H5''" sing N N 122 G "C4'" "O4'" sing N N 123 G "C4'" "C3'" sing N N 124 G "C4'" "H4'" sing N N 125 G "O4'" "C1'" sing N N 126 G "C3'" "O3'" sing N N 127 G "C3'" "C2'" sing N N 128 G "C3'" "H3'" sing N N 129 G "O3'" "HO3'" sing N N 130 G "C2'" "O2'" sing N N 131 G "C2'" "C1'" sing N N 132 G "C2'" "H2'" sing N N 133 G "O2'" "HO2'" sing N N 134 G "C1'" N9 sing N N 135 G "C1'" "H1'" sing N N 136 G N9 C8 sing Y N 137 G N9 C4 sing Y N 138 G C8 N7 doub Y N 139 G C8 H8 sing N N 140 G N7 C5 sing Y N 141 G C5 C6 sing N N 142 G C5 C4 doub Y N 143 G C6 O6 doub N N 144 G C6 N1 sing N N 145 G N1 C2 sing N N 146 G N1 H1 sing N N 147 G C2 N2 sing N N 148 G C2 N3 doub N N 149 G N2 H21 sing N N 150 G N2 H22 sing N N 151 G N3 C4 sing N N 152 HOH O H1 sing N N 153 HOH O H2 sing N N 154 U OP3 P sing N N 155 U OP3 HOP3 sing N N 156 U P OP1 doub N N 157 U P OP2 sing N N 158 U P "O5'" sing N N 159 U OP2 HOP2 sing N N 160 U "O5'" "C5'" sing N N 161 U "C5'" "C4'" sing N N 162 U "C5'" "H5'" sing N N 163 U "C5'" "H5''" sing N N 164 U "C4'" "O4'" sing N N 165 U "C4'" "C3'" sing N N 166 U "C4'" "H4'" sing N N 167 U "O4'" "C1'" sing N N 168 U "C3'" "O3'" sing N N 169 U "C3'" "C2'" sing N N 170 U "C3'" "H3'" sing N N 171 U "O3'" "HO3'" sing N N 172 U "C2'" "O2'" sing N N 173 U "C2'" "C1'" sing N N 174 U "C2'" "H2'" sing N N 175 U "O2'" "HO2'" sing N N 176 U "C1'" N1 sing N N 177 U "C1'" "H1'" sing N N 178 U N1 C2 sing N N 179 U N1 C6 sing N N 180 U C2 O2 doub N N 181 U C2 N3 sing N N 182 U N3 C4 sing N N 183 U N3 H3 sing N N 184 U C4 O4 doub N N 185 U C4 C5 sing N N 186 U C5 C6 doub N N 187 U C5 H5 sing N N 188 U C6 H6 sing N N 189 UFT OP3 P sing N N 190 UFT OP1 P doub N N 191 UFT P OP2 sing N N 192 UFT P "O5'" sing N N 193 UFT OP3 HOP3 sing N N 194 UFT OP2 HOP2 sing N N 195 UFT "O5'" "C5'" sing N N 196 UFT C6 N1 sing N N 197 UFT N1 C2 sing N N 198 UFT N1 "C1'" sing N N 199 UFT C5 C6 doub N N 200 UFT C6 H6 sing N N 201 UFT N3 C2 sing N N 202 UFT C2 O2 doub N N 203 UFT C4 N3 sing N N 204 UFT O4 C4 doub N N 205 UFT C5 C4 sing N N 206 UFT C5 H5 sing N N 207 UFT "C2'" "F2'" sing N N 208 UFT "C3'" "C2'" sing N N 209 UFT "C2'" "C1'" sing N N 210 UFT "C2'" "H2'" sing N N 211 UFT "C5'" "C4'" sing N N 212 UFT "C5'" "H5'" sing N N 213 UFT "C5'" "H5'A" sing N N 214 UFT "C3'" "C4'" sing N N 215 UFT "C4'" "O4'" sing N N 216 UFT "C4'" "H4'" sing N N 217 UFT "O4'" "C1'" sing N N 218 UFT "C1'" "H1'" sing N N 219 UFT "C3'" "O3'" sing N N 220 UFT "C3'" "H3'" sing N N 221 UFT "O3'" "HO3'" sing N N 222 UFT N3 HN3 sing N N 223 # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A A 4 1_555 B UFT 5 1_555 -0.013 -0.029 0.116 4.303 -18.025 9.564 1 A_A104:UFT213_B A 104 ? B 213 ? 20 1 1 A UFT 5 1_555 B A 4 1_555 0.078 -0.183 0.020 -1.478 -10.770 2.382 2 A_UFT105:A212_B A 105 ? B 212 ? 20 1 # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 A _ndb_struct_na_base_pair_step.i_label_comp_id_1 A _ndb_struct_na_base_pair_step.i_label_seq_id_1 4 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 B _ndb_struct_na_base_pair_step.j_label_comp_id_1 UFT _ndb_struct_na_base_pair_step.j_label_seq_id_1 5 _ndb_struct_na_base_pair_step.j_symmetry_1 1_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 UFT _ndb_struct_na_base_pair_step.i_label_seq_id_2 5 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 B _ndb_struct_na_base_pair_step.j_label_comp_id_2 A _ndb_struct_na_base_pair_step.j_label_seq_id_2 4 _ndb_struct_na_base_pair_step.j_symmetry_2 1_555 _ndb_struct_na_base_pair_step.shift -0.710 _ndb_struct_na_base_pair_step.slide -1.293 _ndb_struct_na_base_pair_step.rise 3.369 _ndb_struct_na_base_pair_step.tilt -2.100 _ndb_struct_na_base_pair_step.roll 18.824 _ndb_struct_na_base_pair_step.twist 30.189 _ndb_struct_na_base_pair_step.x_displacement -4.690 _ndb_struct_na_base_pair_step.y_displacement 0.876 _ndb_struct_na_base_pair_step.helical_rise 2.248 _ndb_struct_na_base_pair_step.inclination 32.441 _ndb_struct_na_base_pair_step.tip 3.620 _ndb_struct_na_base_pair_step.helical_twist 35.521 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_A104UFT105:A212UFT213_BB _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 104 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 B _ndb_struct_na_base_pair_step.j_auth_seq_id_1 213 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 105 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 B _ndb_struct_na_base_pair_step.j_auth_seq_id_2 212 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # _atom_sites.entry_id 3P4C _atom_sites.fract_transf_matrix[1][1] 0.024661 _atom_sites.fract_transf_matrix[1][2] 0.014238 _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] 0.028476 _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] 0.008531 _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 F N O P SR # loop_