data_8PFK # _entry.id 8PFK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 8PFK pdb_00008pfk 10.2210/pdb8pfk/pdb WWPDB D_1292131244 ? ? # 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 2024-01-31 2 'Structure model' 1 1 2024-04-24 3 'Structure model' 1 2 2024-05-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' # 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' citation 4 3 'Structure model' citation_author # 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 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation_author.name' 5 3 'Structure model' '_citation.page_first' 6 3 'Structure model' '_citation.page_last' 7 3 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8PFK _pdbx_database_status.recvd_initial_deposition_date 2023-06-16 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email spingler@chem.uzh.ch _pdbx_contact_author.name_first Bernhard _pdbx_contact_author.name_last Spingler _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-3402-2016 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Spingler, B.' 1 0000-0003-3402-2016 'McAuley, K.' 2 0000-0002-9545-072X 'Nievergelt, P.' 3 0000-0001-9602-0417 'Thorn, A.' 4 0000-0003-4503-4258 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country DE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Chemmedchem _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1860-7187 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 19 _citation.language ? _citation.page_first e202300600 _citation.page_last e202300600 _citation.title 'RNA oligomers at atomic resolution containing 1-methylpseudouridine, an essential building block of mRNA vaccines.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/cmdc.202300600 _citation.pdbx_database_id_PubMed 38235959 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nievergelt, P.' 1 0000-0001-9602-0417 primary 'Berliat, F.' 2 ? primary 'McAuley, K.E.' 3 0000-0002-9545-072X primary 'Dorgan, C.R.' 4 ? primary 'van Well, R.M.' 5 ? primary 'Thorn, A.' 6 0000-0003-4503-4258 primary 'Spingler, B.' 7 0000-0003-3402-2016 # 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 'RNA (12-mer)' 3865.387 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 water nat water 18.015 95 ? ? ? ? # _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 'CGCGAA(B8H)UAGCG' _entity_poly.pdbx_seq_one_letter_code_can CGCGAAUUAGCG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 C n 1 4 G n 1 5 A n 1 6 A n 1 7 B8H n 1 8 U n 1 9 A n 1 10 G n 1 11 C n 1 12 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 12 _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 ? # 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 B8H 'RNA linking' n ;[(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate ; ? 'C10 H15 N2 O9 P' 338.208 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 A 6 6 6 A A A . n A 1 7 B8H 7 7 7 B8H B8H A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n A 1 12 G 12 12 12 G G A . 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 B 2 MG 1 101 98 MG MG A . C 2 MG 1 102 99 MG MG A . D 3 HOH 1 201 68 HOH HOH A . D 3 HOH 2 202 93 HOH HOH A . D 3 HOH 3 203 20 HOH HOH A . D 3 HOH 4 204 36 HOH HOH A . D 3 HOH 5 205 60 HOH HOH A . D 3 HOH 6 206 37 HOH HOH A . D 3 HOH 7 207 63 HOH HOH A . D 3 HOH 8 208 72 HOH HOH A . D 3 HOH 9 209 30 HOH HOH A . D 3 HOH 10 210 29 HOH HOH A . D 3 HOH 11 211 8 HOH HOH A . D 3 HOH 12 212 27 HOH HOH A . D 3 HOH 13 213 52 HOH HOH A . D 3 HOH 14 214 41 HOH HOH A . D 3 HOH 15 215 35 HOH HOH A . D 3 HOH 16 216 32 HOH HOH A . D 3 HOH 17 217 33 HOH HOH A . D 3 HOH 18 218 55 HOH HOH A . D 3 HOH 19 219 3 HOH HOH A . D 3 HOH 20 220 17 HOH HOH A . D 3 HOH 21 221 92 HOH HOH A . D 3 HOH 22 222 76 HOH HOH A . D 3 HOH 23 223 94 HOH HOH A . D 3 HOH 24 224 28 HOH HOH A . D 3 HOH 25 225 4 HOH HOH A . D 3 HOH 26 226 91 HOH HOH A . D 3 HOH 27 227 5 HOH HOH A . D 3 HOH 28 228 12 HOH HOH A . D 3 HOH 29 229 49 HOH HOH A . D 3 HOH 30 230 14 HOH HOH A . D 3 HOH 31 231 87 HOH HOH A . D 3 HOH 32 232 23 HOH HOH A . D 3 HOH 33 233 39 HOH HOH A . D 3 HOH 34 234 75 HOH HOH A . D 3 HOH 35 235 2 HOH HOH A . D 3 HOH 36 236 9 HOH HOH A . D 3 HOH 37 237 47 HOH HOH A . D 3 HOH 38 238 26 HOH HOH A . D 3 HOH 39 239 56 HOH HOH A . D 3 HOH 40 240 7 HOH HOH A . D 3 HOH 41 241 79 HOH HOH A . D 3 HOH 42 242 19 HOH HOH A . D 3 HOH 43 243 1 HOH HOH A . D 3 HOH 44 244 16 HOH HOH A . D 3 HOH 45 245 74 HOH HOH A . D 3 HOH 46 246 13 HOH HOH A . D 3 HOH 47 247 10 HOH HOH A . D 3 HOH 48 248 44 HOH HOH A . D 3 HOH 49 249 50 HOH HOH A . D 3 HOH 50 250 15 HOH HOH A . D 3 HOH 51 251 71 HOH HOH A . D 3 HOH 52 252 61 HOH HOH A . D 3 HOH 53 253 51 HOH HOH A . D 3 HOH 54 254 24 HOH HOH A . D 3 HOH 55 255 67 HOH HOH A . D 3 HOH 56 256 48 HOH HOH A . D 3 HOH 57 257 31 HOH HOH A . D 3 HOH 58 258 34 HOH HOH A . D 3 HOH 59 259 83 HOH HOH A . D 3 HOH 60 260 43 HOH HOH A . D 3 HOH 61 261 22 HOH HOH A . D 3 HOH 62 262 85 HOH HOH A . D 3 HOH 63 263 53 HOH HOH A . D 3 HOH 64 264 11 HOH HOH A . D 3 HOH 65 265 21 HOH HOH A . D 3 HOH 66 266 57 HOH HOH A . D 3 HOH 67 267 46 HOH HOH A . D 3 HOH 68 268 40 HOH HOH A . D 3 HOH 69 269 18 HOH HOH A . D 3 HOH 70 270 6 HOH HOH A . D 3 HOH 71 271 81 HOH HOH A . D 3 HOH 72 272 58 HOH HOH A . D 3 HOH 73 273 89 HOH HOH A . D 3 HOH 74 274 90 HOH HOH A . D 3 HOH 75 275 95 HOH HOH A . D 3 HOH 76 276 64 HOH HOH A . D 3 HOH 77 277 80 HOH HOH A . D 3 HOH 78 278 54 HOH HOH A . D 3 HOH 79 279 66 HOH HOH A . D 3 HOH 80 280 65 HOH HOH A . D 3 HOH 81 281 73 HOH HOH A . D 3 HOH 82 282 42 HOH HOH A . D 3 HOH 83 283 38 HOH HOH A . D 3 HOH 84 284 82 HOH HOH A . D 3 HOH 85 285 70 HOH HOH A . D 3 HOH 86 286 62 HOH HOH A . D 3 HOH 87 287 84 HOH HOH A . D 3 HOH 88 288 88 HOH HOH A . D 3 HOH 89 289 86 HOH HOH A . D 3 HOH 90 290 69 HOH HOH A . D 3 HOH 91 291 59 HOH HOH A . D 3 HOH 92 292 77 HOH HOH A . D 3 HOH 93 293 78 HOH HOH A . D 3 HOH 94 294 45 HOH HOH A . D 3 HOH 95 295 25 HOH HOH A . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 128.070 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 8PFK _cell.details ? _cell.formula_units_Z ? _cell.length_a 41.295 _cell.length_a_esd ? _cell.length_b 34.777 _cell.length_b_esd ? _cell.length_c 31.685 _cell.length_c_esd ? _cell.volume 35822.870 _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8PFK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8PFK _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.32 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 46.91 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '10 % v/v MPD, 40 mM sodium cacodylate, 12 mM spermine, 80 mM sodium chloride, 12 mM potassium chloride and 20 mM magnesium chloride' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 298 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 2M-F' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2022-02-09 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SLS BEAMLINE X06SA' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.000 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline X06SA _diffrn_source.pdbx_synchrotron_site SLS # _reflns.B_iso_Wilson_estimate 14.19 _reflns.entry_id 8PFK _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.321 _reflns.d_resolution_low 23.75 _reflns.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.number_all ? _reflns.number_obs 14352 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 89.52 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 1.9 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 24.01 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.02231 _reflns.pdbx_Rpim_I_all 0.01578 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.01578 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 1.321 _reflns_shell.d_res_low 1.368 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.11 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 315 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 1.1 _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 0.4744 _reflns_shell.pdbx_Rpim_I_all 0.3354 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.831 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all 37.65 _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.3354 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 20.29 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8PFK _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.321 _refine.ls_d_res_low 23.75 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 7504 _refine.ls_number_reflns_R_free 376 _refine.ls_number_reflns_R_work 7128 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 89.16 _refine.ls_percent_reflns_R_free 5.01 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1469 _refine.ls_R_factor_R_free 0.1832 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1451 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.38 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 26.7672 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.0926 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.321 _refine_hist.d_res_low 23.75 _refine_hist.number_atoms_solvent 95 _refine_hist.number_atoms_total 353 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 256 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0055 ? 286 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.9497 ? 445 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0337 ? 58 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0107 ? 12 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 6.5660 ? 134 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.321 1.51 . . 95 1802 67.90 . . . . 0.1719 . . . . . . . . . . . 0.2493 'X-RAY DIFFRACTION' 1.51 1.90 . . 139 2632 99.60 . . . . 0.1590 . . . . . . . . . . . 0.1598 'X-RAY DIFFRACTION' 1.90 23.75 . . 142 2694 99.86 . . . . 0.1376 . . . . . . . . . . . 0.1840 # _struct.entry_id 8PFK _struct.title 'RNA structure with 1-methylpseudoridine, C2 space group' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8PFK _struct_keywords.text 'SARS-CoV-2, COVID-19, Coronavirus, mRNA vaccine, RNA' _struct_keywords.pdbx_keywords RNA # 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 2 ? C N N 2 ? D N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8PFK _struct_ref.pdbx_db_accession 8PFK _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8PFK _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 8PFK _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # 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 'point symmetry operation' ? ? -1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 0.0 2 'identity operation' 1_555 x,y,z 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 3 'identity operation' 1_555 x,y,z 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 # 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 A 6 "O3'" ? ? ? 1_555 A B8H 7 P ? ? A A 6 A B8H 7 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale2 covale one ? A B8H 7 "O3'" ? ? ? 1_555 A U 8 P ? ? A B8H 7 A U 8 1_555 ? ? ? ? ? ? ? 1.607 ? ? metalc1 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 211 1_555 ? ? ? ? ? ? ? 2.218 ? ? metalc2 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 227 1_555 ? ? ? ? ? ? ? 2.114 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 242 1_555 ? ? ? ? ? ? ? 1.927 ? ? metalc4 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 282 1_555 ? ? ? ? ? ? ? 2.228 ? ? metalc5 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 289 1_555 ? ? ? ? ? ? ? 2.117 ? ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 295 1_555 ? ? ? ? ? ? ? 2.083 ? ? metalc7 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 235 1_555 ? ? ? ? ? ? ? 2.063 ? ? metalc8 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 243 1_555 ? ? ? ? ? ? ? 2.040 ? ? metalc9 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 254 1_555 ? ? ? ? ? ? ? 2.773 ? ? metalc10 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 269 2_555 ? ? ? ? ? ? ? 2.084 ? ? metalc11 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 283 1_555 ? ? ? ? ? ? ? 2.204 ? ? metalc12 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 102 A HOH 291 2_555 ? ? ? ? ? ? ? 2.053 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 12 N1 ? ? A C 1 A G 12 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 12 O6 ? ? A C 1 A G 12 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 12 N2 ? ? A C 1 A G 12 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 11 N3 ? ? A G 2 A C 11 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 11 O2 ? ? A G 2 A C 11 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 11 N4 ? ? A G 2 A C 11 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 10 N1 ? ? A C 3 A G 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 10 O6 ? ? A C 3 A G 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 10 N2 ? ? A C 3 A G 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 A A 9 N1 ? ? A G 4 A A 9 2_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A A 9 N6 ? ? A G 4 A A 9 2_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 8 N3 ? ? A A 5 A U 8 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 8 O4 ? ? A A 5 A U 8 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 6 N1 ? ? ? 1_555 A B8H 7 N3 ? ? A A 6 A B8H 7 2_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog15 hydrog ? ? A A 6 N6 ? ? ? 1_555 A B8H 7 O2 ? ? A A 6 A B8H 7 2_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog16 hydrog ? ? A B8H 7 N3 ? ? ? 1_555 A A 6 N1 ? ? A B8H 7 A A 6 2_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog17 hydrog ? ? A B8H 7 O2 ? ? ? 1_555 A A 6 N6 ? ? A B8H 7 A A 6 2_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog18 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 5 N1 ? ? A U 8 A A 5 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 5 N6 ? ? A U 8 A A 5 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 9 N1 ? ? ? 1_555 A G 4 N1 ? ? A A 9 A G 4 2_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog21 hydrog ? ? A A 9 N6 ? ? ? 1_555 A G 4 O6 ? ? A A 9 A G 4 2_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog22 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 3 N3 ? ? A G 10 A C 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 3 O2 ? ? A G 10 A C 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 3 N4 ? ? A G 10 A C 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 2 N1 ? ? A C 11 A G 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 2 O6 ? ? A C 11 A G 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 2 N2 ? ? A C 11 A G 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 1 N3 ? ? A G 12 A C 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 1 O2 ? ? A G 12 A C 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 1 N4 ? ? A G 12 A C 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 211 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 227 ? 1_555 89.8 ? 2 O ? D HOH . ? A HOH 211 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 242 ? 1_555 85.4 ? 3 O ? D HOH . ? A HOH 227 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 242 ? 1_555 91.9 ? 4 O ? D HOH . ? A HOH 211 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 282 ? 1_555 90.3 ? 5 O ? D HOH . ? A HOH 227 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 282 ? 1_555 85.0 ? 6 O ? D HOH . ? A HOH 242 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 282 ? 1_555 174.8 ? 7 O ? D HOH . ? A HOH 211 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 289 ? 1_555 176.3 ? 8 O ? D HOH . ? A HOH 227 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 289 ? 1_555 93.5 ? 9 O ? D HOH . ? A HOH 242 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 289 ? 1_555 96.1 ? 10 O ? D HOH . ? A HOH 282 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 289 ? 1_555 88.3 ? 11 O ? D HOH . ? A HOH 211 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 84.6 ? 12 O ? D HOH . ? A HOH 227 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 174.4 ? 13 O ? D HOH . ? A HOH 242 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 87.3 ? 14 O ? D HOH . ? A HOH 282 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 95.3 ? 15 O ? D HOH . ? A HOH 289 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 92.1 ? 16 O ? D HOH . ? A HOH 235 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 243 ? 1_555 89.1 ? 17 O ? D HOH . ? A HOH 235 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 254 ? 1_555 86.7 ? 18 O ? D HOH . ? A HOH 243 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 254 ? 1_555 69.1 ? 19 O ? D HOH . ? A HOH 235 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 269 ? 2_555 84.0 ? 20 O ? D HOH . ? A HOH 243 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 269 ? 2_555 172.6 ? 21 O ? D HOH . ? A HOH 254 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 269 ? 2_555 107.5 ? 22 O ? D HOH . ? A HOH 235 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 283 ? 1_555 87.5 ? 23 O ? D HOH . ? A HOH 243 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 283 ? 1_555 90.3 ? 24 O ? D HOH . ? A HOH 254 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 283 ? 1_555 158.6 ? 25 O ? D HOH . ? A HOH 269 ? 2_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 283 ? 1_555 92.3 ? 26 O ? D HOH . ? A HOH 235 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 291 ? 2_555 175.5 ? 27 O ? D HOH . ? A HOH 243 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 291 ? 2_555 88.6 ? 28 O ? D HOH . ? A HOH 254 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 291 ? 2_555 96.2 ? 29 O ? D HOH . ? A HOH 269 ? 2_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 291 ? 2_555 98.4 ? 30 O ? D HOH . ? A HOH 283 ? 1_555 MG ? C MG . ? A MG 102 ? 1_555 O ? D HOH . ? A HOH 291 ? 2_555 88.5 ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 221 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 250 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 3_556 _pdbx_validate_symm_contact.dist 2.12 # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -x,y,-z 3 x+1/2,y+1/2,z 4 -x+1/2,y+1/2,-z # _pdbx_entry_details.entry_id 8PFK _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y # 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 B8H N1 N N N 38 B8H C2 C N N 39 B8H C4 C N N 40 B8H "C1'" C N S 41 B8H "C2'" C N R 42 B8H "C3'" C N S 43 B8H "C4'" C N R 44 B8H C5 C N N 45 B8H "C5'" C N N 46 B8H C6 C N N 47 B8H CN1 C N N 48 B8H N3 N N N 49 B8H O2 O N N 50 B8H "O2'" O N N 51 B8H "O3'" O N N 52 B8H O4 O N N 53 B8H "O4'" O N N 54 B8H "O5'" O N N 55 B8H OP1 O N N 56 B8H OP2 O N N 57 B8H P P N N 58 B8H O1 O N N 59 B8H H1 H N N 60 B8H H2 H N N 61 B8H H3 H N N 62 B8H H4 H N N 63 B8H H5 H N N 64 B8H H6 H N N 65 B8H H7 H N N 66 B8H H8 H N N 67 B8H H9 H N N 68 B8H H10 H N N 69 B8H H11 H N N 70 B8H H12 H N N 71 B8H H13 H N N 72 B8H H14 H N N 73 B8H H15 H N N 74 C OP3 O N N 75 C P P N N 76 C OP1 O N N 77 C OP2 O N N 78 C "O5'" O N N 79 C "C5'" C N N 80 C "C4'" C N R 81 C "O4'" O N N 82 C "C3'" C N S 83 C "O3'" O N N 84 C "C2'" C N R 85 C "O2'" O N N 86 C "C1'" C N R 87 C N1 N N N 88 C C2 C N N 89 C O2 O N N 90 C N3 N N N 91 C C4 C N N 92 C N4 N N N 93 C C5 C N N 94 C C6 C N N 95 C HOP3 H N N 96 C HOP2 H N N 97 C "H5'" H N N 98 C "H5''" H N N 99 C "H4'" H N N 100 C "H3'" H N N 101 C "HO3'" H N N 102 C "H2'" H N N 103 C "HO2'" H N N 104 C "H1'" H N N 105 C H41 H N N 106 C H42 H N N 107 C H5 H N N 108 C H6 H N N 109 G OP3 O N N 110 G P P N N 111 G OP1 O N N 112 G OP2 O N N 113 G "O5'" O N N 114 G "C5'" C N N 115 G "C4'" C N R 116 G "O4'" O N N 117 G "C3'" C N S 118 G "O3'" O N N 119 G "C2'" C N R 120 G "O2'" O N N 121 G "C1'" C N R 122 G N9 N Y N 123 G C8 C Y N 124 G N7 N Y N 125 G C5 C Y N 126 G C6 C N N 127 G O6 O N N 128 G N1 N N N 129 G C2 C N N 130 G N2 N N N 131 G N3 N N N 132 G C4 C Y N 133 G HOP3 H N N 134 G HOP2 H N N 135 G "H5'" H N N 136 G "H5''" H N N 137 G "H4'" H N N 138 G "H3'" H N N 139 G "HO3'" H N N 140 G "H2'" H N N 141 G "HO2'" H N N 142 G "H1'" H N N 143 G H8 H N N 144 G H1 H N N 145 G H21 H N N 146 G H22 H N N 147 HOH O O N N 148 HOH H1 H N N 149 HOH H2 H N N 150 MG MG MG N N 151 U OP3 O N N 152 U P P N N 153 U OP1 O N N 154 U OP2 O N N 155 U "O5'" O N N 156 U "C5'" C N N 157 U "C4'" C N R 158 U "O4'" O N N 159 U "C3'" C N S 160 U "O3'" O N N 161 U "C2'" C N R 162 U "O2'" O N N 163 U "C1'" C N R 164 U N1 N N N 165 U C2 C N N 166 U O2 O N N 167 U N3 N N N 168 U C4 C N N 169 U O4 O N N 170 U C5 C N N 171 U C6 C N N 172 U HOP3 H N N 173 U HOP2 H N N 174 U "H5'" H N N 175 U "H5''" H N N 176 U "H4'" H N N 177 U "H3'" H N N 178 U "HO3'" H N N 179 U "H2'" H N N 180 U "HO2'" H N N 181 U "H1'" H N N 182 U H3 H N N 183 U H5 H N N 184 U H6 H N N 185 # 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 B8H "C5'" "C4'" sing N N 40 B8H "C5'" "O5'" sing N N 41 B8H "C4'" "O4'" sing N N 42 B8H "C4'" "C3'" sing N N 43 B8H OP2 P doub N N 44 B8H "O2'" "C2'" sing N N 45 B8H "O4'" "C1'" sing N N 46 B8H "O3'" "C3'" sing N N 47 B8H P "O5'" sing N N 48 B8H P OP1 sing N N 49 B8H "C3'" "C2'" sing N N 50 B8H "C1'" "C2'" sing N N 51 B8H "C1'" C5 sing N N 52 B8H C5 C6 doub N N 53 B8H C5 C4 sing N N 54 B8H O4 C4 doub N N 55 B8H C6 N1 sing N N 56 B8H C4 N3 sing N N 57 B8H N1 CN1 sing N N 58 B8H N1 C2 sing N N 59 B8H N3 C2 sing N N 60 B8H C2 O2 doub N N 61 B8H P O1 sing N N 62 B8H "C1'" H1 sing N N 63 B8H "C2'" H2 sing N N 64 B8H "C3'" H3 sing N N 65 B8H "C4'" H4 sing N N 66 B8H "C5'" H5 sing N N 67 B8H "C5'" H6 sing N N 68 B8H C6 H7 sing N N 69 B8H CN1 H8 sing N N 70 B8H CN1 H9 sing N N 71 B8H CN1 H10 sing N N 72 B8H N3 H11 sing N N 73 B8H "O2'" H12 sing N N 74 B8H "O3'" H13 sing N N 75 B8H OP1 H14 sing N N 76 B8H O1 H15 sing N N 77 C OP3 P sing N N 78 C OP3 HOP3 sing N N 79 C P OP1 doub N N 80 C P OP2 sing N N 81 C P "O5'" sing N N 82 C OP2 HOP2 sing N N 83 C "O5'" "C5'" sing N N 84 C "C5'" "C4'" sing N N 85 C "C5'" "H5'" sing N N 86 C "C5'" "H5''" sing N N 87 C "C4'" "O4'" sing N N 88 C "C4'" "C3'" sing N N 89 C "C4'" "H4'" sing N N 90 C "O4'" "C1'" sing N N 91 C "C3'" "O3'" sing N N 92 C "C3'" "C2'" sing N N 93 C "C3'" "H3'" sing N N 94 C "O3'" "HO3'" sing N N 95 C "C2'" "O2'" sing N N 96 C "C2'" "C1'" sing N N 97 C "C2'" "H2'" sing N N 98 C "O2'" "HO2'" sing N N 99 C "C1'" N1 sing N N 100 C "C1'" "H1'" sing N N 101 C N1 C2 sing N N 102 C N1 C6 sing N N 103 C C2 O2 doub N N 104 C C2 N3 sing N N 105 C N3 C4 doub N N 106 C C4 N4 sing N N 107 C C4 C5 sing N N 108 C N4 H41 sing N N 109 C N4 H42 sing N N 110 C C5 C6 doub N N 111 C C5 H5 sing N N 112 C C6 H6 sing N N 113 G OP3 P sing N N 114 G OP3 HOP3 sing N N 115 G P OP1 doub N N 116 G P OP2 sing N N 117 G P "O5'" sing N N 118 G OP2 HOP2 sing N N 119 G "O5'" "C5'" sing N N 120 G "C5'" "C4'" sing N N 121 G "C5'" "H5'" sing N N 122 G "C5'" "H5''" sing N N 123 G "C4'" "O4'" sing N N 124 G "C4'" "C3'" sing N N 125 G "C4'" "H4'" sing N N 126 G "O4'" "C1'" sing N N 127 G "C3'" "O3'" sing N N 128 G "C3'" "C2'" sing N N 129 G "C3'" "H3'" sing N N 130 G "O3'" "HO3'" sing N N 131 G "C2'" "O2'" sing N N 132 G "C2'" "C1'" sing N N 133 G "C2'" "H2'" sing N N 134 G "O2'" "HO2'" sing N N 135 G "C1'" N9 sing N N 136 G "C1'" "H1'" sing N N 137 G N9 C8 sing Y N 138 G N9 C4 sing Y N 139 G C8 N7 doub Y N 140 G C8 H8 sing N N 141 G N7 C5 sing Y N 142 G C5 C6 sing N N 143 G C5 C4 doub Y N 144 G C6 O6 doub N N 145 G C6 N1 sing N N 146 G N1 C2 sing N N 147 G N1 H1 sing N N 148 G C2 N2 sing N N 149 G C2 N3 doub N N 150 G N2 H21 sing N N 151 G N2 H22 sing N N 152 G N3 C4 sing N N 153 HOH O H1 sing N N 154 HOH O H2 sing N N 155 U OP3 P sing N N 156 U OP3 HOP3 sing N N 157 U P OP1 doub N N 158 U P OP2 sing N N 159 U P "O5'" sing N N 160 U OP2 HOP2 sing N N 161 U "O5'" "C5'" sing N N 162 U "C5'" "C4'" sing N N 163 U "C5'" "H5'" sing N N 164 U "C5'" "H5''" sing N N 165 U "C4'" "O4'" sing N N 166 U "C4'" "C3'" sing N N 167 U "C4'" "H4'" sing N N 168 U "O4'" "C1'" sing N N 169 U "C3'" "O3'" sing N N 170 U "C3'" "C2'" sing N N 171 U "C3'" "H3'" sing N N 172 U "O3'" "HO3'" sing N N 173 U "C2'" "O2'" sing N N 174 U "C2'" "C1'" sing N N 175 U "C2'" "H2'" sing N N 176 U "O2'" "HO2'" sing N N 177 U "C1'" N1 sing N N 178 U "C1'" "H1'" sing N N 179 U N1 C2 sing N N 180 U N1 C6 sing N N 181 U C2 O2 doub N N 182 U C2 N3 sing N N 183 U N3 C4 sing N N 184 U N3 H3 sing N N 185 U C4 O4 doub N N 186 U C4 C5 sing N N 187 U C5 C6 doub N N 188 U C5 H5 sing N N 189 U C6 H6 sing N N 190 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8PFK 'double helix' 8PFK 'a-form double helix' 8PFK 'mismatched base pair' # 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 C 1 1_555 A G 12 2_555 0.144 -0.087 0.054 7.788 -15.316 -0.403 1 A_C1:G12_A A 1 ? A 12 ? 19 1 1 A G 2 1_555 A C 11 2_555 -0.284 -0.151 0.040 -6.375 -17.685 1.415 2 A_G2:C11_A A 2 ? A 11 ? 19 1 1 A C 3 1_555 A G 10 2_555 0.123 -0.125 0.358 -3.390 -13.503 -2.925 3 A_C3:G10_A A 3 ? A 10 ? 19 1 1 A G 4 1_555 A A 9 2_555 -0.037 1.466 -0.372 4.194 -9.070 -17.419 4 A_G4:A9_A A 4 ? A 9 ? 8 1 1 A A 5 1_555 A U 8 2_555 0.120 -0.027 0.160 1.007 -14.734 -5.723 5 A_A5:U8_A A 5 ? A 8 ? 20 1 1 A A 6 1_555 A B8H 7 2_555 0.086 1.273 -0.121 25.329 -0.096 168.423 6 A_A6:B8H7_A A 6 ? A 7 ? 21 1 1 A B8H 7 1_555 A A 6 2_555 -0.086 -1.273 0.121 -25.329 0.096 -168.423 7 A_B8H7:A6_A A 7 ? A 6 ? 21 1 1 A U 8 1_555 A A 5 2_555 -0.120 -0.027 0.160 -1.007 -14.734 -5.723 8 A_U8:A5_A A 8 ? A 5 ? 20 1 1 A A 9 1_555 A G 4 2_555 0.037 1.466 -0.372 -4.194 -9.070 -17.419 9 A_A9:G4_A A 9 ? A 4 ? 8 1 1 A G 10 1_555 A C 3 2_555 -0.123 -0.125 0.358 3.390 -13.503 -2.925 10 A_G10:C3_A A 10 ? A 3 ? 19 1 1 A C 11 1_555 A G 2 2_555 0.284 -0.151 0.040 6.375 -17.685 1.415 11 A_C11:G2_A A 11 ? A 2 ? 19 1 1 A G 12 1_555 A C 1 2_555 -0.144 -0.087 0.054 -7.788 -15.316 -0.403 12 A_G12:C1_A A 12 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 1 1_555 A G 12 2_555 A G 2 1_555 A C 11 2_555 -0.371 -1.661 3.428 -2.227 12.018 33.348 -4.434 0.294 2.706 20.121 3.728 35.458 1 AA_C1G2:C11G12_AA A 1 ? A 12 ? A 2 ? A 11 ? 1 A G 2 1_555 A C 11 2_555 A C 3 1_555 A G 10 2_555 -0.465 -1.363 3.162 -2.967 3.768 34.457 -2.827 0.347 3.029 6.322 4.978 34.779 2 AA_G2C3:G10C11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A C 3 1_555 A G 10 2_555 A G 4 1_555 A A 9 2_555 -0.904 -1.408 3.084 4.149 9.574 25.851 -4.870 2.721 2.259 20.375 -8.831 27.844 3 AA_C3G4:A9G10_AA A 3 ? A 10 ? A 4 ? A 9 ? 1 A G 4 1_555 A A 9 2_555 A A 5 1_555 A U 8 2_555 0.429 -1.717 3.218 -4.637 14.448 30.420 -4.949 -1.379 2.123 25.629 8.226 33.914 4 AA_G4A5:U8A9_AA A 4 ? A 9 ? A 5 ? A 8 ? 1 A A 5 1_555 A U 8 2_555 A A 6 1_555 A B8H 7 2_555 0.643 -1.071 3.300 -4.090 7.376 -48.865 0.711 0.452 3.457 -8.840 -4.901 -49.543 5 AA_A5A6:B8H7U8_AA A 5 ? A 8 ? A 6 ? A 7 ? 1 A A 6 1_555 A B8H 7 2_555 A B8H 7 1_555 A A 6 2_555 3.387 -0.979 0.000 29.135 -169.627 180.000 -0.490 -1.693 0.000 -84.814 -14.568 180.000 6 AA_A6B8H7:A6B8H7_AA A 6 ? A 7 ? A 7 ? A 6 ? 1 A B8H 7 1_555 A A 6 2_555 A U 8 1_555 A A 5 2_555 -2.501 2.488 -0.043 -156.203 -70.963 -121.988 -1.281 -1.171 -0.641 35.700 -78.581 -175.913 7 AA_B8H7U8:A5A6_AA A 7 ? A 6 ? A 8 ? A 5 ? 1 A U 8 1_555 A A 5 2_555 A A 9 1_555 A G 4 2_555 -0.429 -1.717 3.218 4.637 14.448 30.420 -4.949 1.379 2.123 25.629 -8.226 33.914 8 AA_U8A9:G4A5_AA A 8 ? A 5 ? A 9 ? A 4 ? 1 A A 9 1_555 A G 4 2_555 A G 10 1_555 A C 3 2_555 0.904 -1.408 3.084 -4.149 9.574 25.851 -4.870 -2.721 2.259 20.375 8.831 27.844 9 AA_A9G10:C3G4_AA A 9 ? A 4 ? A 10 ? A 3 ? 1 A G 10 1_555 A C 3 2_555 A C 11 1_555 A G 2 2_555 0.465 -1.363 3.162 2.967 3.768 34.457 -2.827 -0.347 3.029 6.322 -4.978 34.779 10 AA_G10C11:G2C3_AA A 10 ? A 3 ? A 11 ? A 2 ? 1 A C 11 1_555 A G 2 2_555 A G 12 1_555 A C 1 2_555 0.371 -1.661 3.428 2.227 12.018 33.348 -4.434 -0.294 2.706 20.121 -3.728 35.458 11 AA_C11G12:C1G2_AA A 11 ? A 2 ? A 12 ? A 1 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'University of Zurich' Switzerland ? 1 'Swiss National Science Foundation' Switzerland 206021_164018 2 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id B8H _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id B8H _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 157D _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'C 1 2 1' _space_group.name_Hall 'C 2y' _space_group.IT_number 5 _space_group.crystal_system monoclinic _space_group.id 1 # _atom_sites.entry_id 8PFK _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.024216 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.018967 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.028755 _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] 0.040089 _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_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.51345 0.48472 ? ? 24.73122 6.32584 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? MG ? ? 9.41153 2.53737 ? ? 2.59044 63.03566 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_