data_3P4D # _entry.id 3P4D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 3P4D pdb_00003p4d 10.2210/pdb3p4d/pdb NDB NA0812 ? ? RCSB RCSB061940 ? ? WWPDB D_1000061940 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3P4B . unspecified PDB 3P4C . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3P4D _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # 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 ? # _cell.entry_id 3P4D _cell.length_a 41.630 _cell.length_b 41.630 _cell.length_c 126.489 _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 3P4D _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 ? # 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*CP*(CFZ)P*CP*(GF2)P*GP*(GF2)P*G)-3'" 2564.557 2 ? ? ? ? 2 water nat water 18.015 28 ? ? ? ? # _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)C(CFZ)C(GF2)G(GF2)G' _entity_poly.pdbx_seq_one_letter_code_can XCXCXGXG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 CFZ n 1 2 C n 1 3 CFZ n 1 4 C n 1 5 GF2 n 1 6 G n 1 7 GF2 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized modified RNA octamer' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3P4D _struct_ref.pdbx_db_accession 3P4D _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code XCXCXGXG _struct_ref.pdbx_db_isoform ? # 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 3P4D A 1 ? 8 ? 3P4D 101 ? 108 ? 101 108 2 1 3P4D B 1 ? 8 ? 3P4D 201 ? 208 ? 201 208 # 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 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 GF2 'DNA linking' n ;2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate) ; ? 'C10 H13 F N5 O7 P' 365.212 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 3P4D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.06 _exptl_crystal.density_percent_sol 40.18 _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), sodium 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 225 mm CCD' _diffrn_detector.pdbx_collection_date 2008-11-17 _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 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97872 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 21-ID-F' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 21-ID-F _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97872 # _reflns.entry_id 3P4D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30 _reflns.d_resolution_high 1.85 _reflns.number_obs 3824 _reflns.number_all 3843 _reflns.percent_possible_obs 99.5 _reflns.pdbx_Rmerge_I_obs 0.077 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 28.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 13.9 _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 1.85 _reflns_shell.d_res_low 1.92 _reflns_shell.percent_possible_all 99.7 _reflns_shell.Rmerge_I_obs 0.43 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 6.9 _reflns_shell.pdbx_redundancy 14.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 370 _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 3P4D _refine.ls_number_reflns_obs 3544 _refine.ls_number_reflns_all ? _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 21.08 _refine.ls_d_res_high 1.85 _refine.ls_percent_reflns_obs 100.00 _refine.ls_R_factor_obs 0.21426 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20960 _refine.ls_R_factor_R_free 0.27115 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.3 _refine.ls_number_reflns_R_free 280 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.949 _refine.B_iso_mean 32.878 _refine.aniso_B[1][1] -1.15 _refine.aniso_B[2][2] -1.15 _refine.aniso_B[3][3] 1.73 _refine.aniso_B[1][2] -0.58 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 1RXB' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free 0.166 _refine.overall_SU_ML 0.122 _refine.overall_SU_B 8.824 _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 ? _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 338 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 28 _refine_hist.number_atoms_total 366 _refine_hist.d_res_high 1.85 _refine_hist.d_res_low 21.08 # 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 r_bond_refined_d 0.011 0.021 ? 376 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.124 3.000 ? 584 'X-RAY DIFFRACTION' ? r_chiral_restr 0.103 0.200 ? 78 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.015 0.020 ? 168 'X-RAY DIFFRACTION' ? r_scbond_it 2.175 3.000 ? 376 'X-RAY DIFFRACTION' ? r_scangle_it 2.765 4.500 ? 584 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.85 _refine_ls_shell.d_res_low 1.896 _refine_ls_shell.number_reflns_R_work 243 _refine_ls_shell.R_factor_R_work 0.243 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.351 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 23 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 243 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3P4D _struct.title ;Alternatingly modified 2'Fluoro RNA octamer f/rC4G4 ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3P4D _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;RNA, 2'-FLUORO-RNA, O2'-MODIFICATION, OCTAMER, 2'-fluoro 2'-deoxycytidine, 2'-fluoro 2'-deoxyguanosine, 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 ? # _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 C 2 P ? ? A CFZ 101 A C 102 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale2 covale both ? A C 2 "O3'" ? ? ? 1_555 A CFZ 3 P ? ? A C 102 A CFZ 103 1_555 ? ? ? ? ? ? ? 1.588 ? ? covale3 covale both ? A CFZ 3 "O3'" ? ? ? 1_555 A C 4 P ? ? A CFZ 103 A C 104 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale4 covale both ? A C 4 "O3'" ? ? ? 1_555 A GF2 5 P ? ? A C 104 A GF2 105 1_555 ? ? ? ? ? ? ? 1.585 ? ? covale5 covale one ? A GF2 5 "O3'" ? ? ? 1_555 A G 6 P ? ? A GF2 105 A G 106 1_555 ? ? ? ? ? ? ? 1.588 ? ? covale6 covale both ? A G 6 "O3'" ? ? ? 1_555 A GF2 7 P ? ? A G 106 A GF2 107 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale7 covale one ? A GF2 7 "O3'" ? ? ? 1_555 A G 8 P ? ? A GF2 107 A G 108 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale8 covale both ? B CFZ 1 "O3'" ? ? ? 1_555 B C 2 P ? ? B CFZ 201 B C 202 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale9 covale both ? B C 2 "O3'" ? ? ? 1_555 B CFZ 3 P ? ? B C 202 B CFZ 203 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale10 covale both ? B CFZ 3 "O3'" ? ? ? 1_555 B C 4 P ? ? B CFZ 203 B C 204 1_555 ? ? ? ? ? ? ? 1.573 ? ? covale11 covale both ? B C 4 "O3'" ? ? ? 1_555 B GF2 5 P ? ? B C 204 B GF2 205 1_555 ? ? ? ? ? ? ? 1.582 ? ? covale12 covale one ? B GF2 5 "O3'" ? ? ? 1_555 B G 6 P ? ? B GF2 205 B G 206 1_555 ? ? ? ? ? ? ? 1.579 ? ? covale13 covale both ? B G 6 "O3'" ? ? ? 1_555 B GF2 7 P ? ? B G 206 B GF2 207 1_555 ? ? ? ? ? ? ? 1.582 ? ? covale14 covale one ? B GF2 7 "O3'" ? ? ? 1_555 B G 8 P ? ? B GF2 207 B G 208 1_555 ? ? ? ? ? ? ? 1.569 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 3P4D _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3P4D _atom_sites.fract_transf_matrix[1][1] 0.024021 _atom_sites.fract_transf_matrix[1][2] 0.013869 _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] 0.027737 _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] 0.007906 _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 # 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 C 2 102 102 C C A . n A 1 3 CFZ 3 103 103 CFZ CFZ A . n A 1 4 C 4 104 104 C C A . n A 1 5 GF2 5 105 105 GF2 GF2 A . n A 1 6 G 6 106 106 G G A . n A 1 7 GF2 7 107 107 GF2 GF2 A . n A 1 8 G 8 108 108 G G A . n B 1 1 CFZ 1 201 201 CFZ CFZ B . n B 1 2 C 2 202 202 C C B . n B 1 3 CFZ 3 203 203 CFZ CFZ B . n B 1 4 C 4 204 204 C C B . n B 1 5 GF2 5 205 205 GF2 GF2 B . n B 1 6 G 6 206 206 G G B . n B 1 7 GF2 7 207 207 GF2 GF2 B . n B 1 8 G 8 208 208 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 HOH 1 7 7 HOH HOH A . C 2 HOH 2 8 8 HOH HOH A . C 2 HOH 3 9 9 HOH HOH A . C 2 HOH 4 10 10 HOH HOH A . C 2 HOH 5 15 15 HOH HOH A . C 2 HOH 6 18 18 HOH HOH A . C 2 HOH 7 19 19 HOH HOH A . C 2 HOH 8 20 20 HOH HOH A . C 2 HOH 9 21 21 HOH HOH A . C 2 HOH 10 22 22 HOH HOH A . C 2 HOH 11 23 23 HOH HOH A . C 2 HOH 12 25 25 HOH HOH A . C 2 HOH 13 26 26 HOH HOH A . C 2 HOH 14 27 27 HOH HOH A . D 2 HOH 1 1 1 HOH HOH B . D 2 HOH 2 2 2 HOH HOH B . D 2 HOH 3 3 3 HOH HOH B . D 2 HOH 4 4 4 HOH HOH B . D 2 HOH 5 5 5 HOH HOH B . D 2 HOH 6 6 6 HOH HOH B . D 2 HOH 7 11 11 HOH HOH B . D 2 HOH 8 12 12 HOH HOH B . D 2 HOH 9 13 13 HOH HOH B . D 2 HOH 10 14 14 HOH HOH B . D 2 HOH 11 16 16 HOH HOH B . D 2 HOH 12 17 17 HOH HOH B . D 2 HOH 13 24 24 HOH HOH B . D 2 HOH 14 28 28 HOH HOH B . # 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 CFZ 3 A CFZ 103 ? DC ? 3 A GF2 5 A GF2 105 ? DG ? 4 A GF2 7 A GF2 107 ? DG ? 5 B CFZ 1 B CFZ 201 ? DC ? 6 B CFZ 3 B CFZ 203 ? DC ? 7 B GF2 5 B GF2 205 ? DG ? 8 B GF2 7 B GF2 207 ? DG ? # _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 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_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 A HOH 15 ? C HOH . 2 1 B HOH 13 ? D HOH . # 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 2023-09-06 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn # 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' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 10.6376 _pdbx_refine_tls.origin_y 9.3828 _pdbx_refine_tls.origin_z 9.8008 _pdbx_refine_tls.T[1][1] 0.0474 _pdbx_refine_tls.T[2][2] 0.0712 _pdbx_refine_tls.T[3][3] 0.0929 _pdbx_refine_tls.T[1][2] 0.0038 _pdbx_refine_tls.T[1][3] 0.0304 _pdbx_refine_tls.T[2][3] 0.0313 _pdbx_refine_tls.L[1][1] 2.8079 _pdbx_refine_tls.L[2][2] 2.8223 _pdbx_refine_tls.L[3][3] 1.0145 _pdbx_refine_tls.L[1][2] 0.5057 _pdbx_refine_tls.L[1][3] -0.4315 _pdbx_refine_tls.L[2][3] 0.7585 _pdbx_refine_tls.S[1][1] 0.1501 _pdbx_refine_tls.S[1][2] -0.2224 _pdbx_refine_tls.S[1][3] -0.1464 _pdbx_refine_tls.S[2][1] 0.1378 _pdbx_refine_tls.S[2][2] -0.0481 _pdbx_refine_tls.S[2][3] 0.2360 _pdbx_refine_tls.S[3][1] -0.0893 _pdbx_refine_tls.S[3][2] -0.0368 _pdbx_refine_tls.S[3][3] -0.1020 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 B 1 B 28 ? . . . . ? 'X-RAY DIFFRACTION' 2 1 A 7 A 27 ? . . . . ? 'X-RAY DIFFRACTION' 3 1 B 201 B 208 ? . . . . ? 'X-RAY DIFFRACTION' 4 1 A 101 A 108 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 MOLREP phasing . ? 2 CCP4 'model building' . ? 3 REFMAC refinement 5.5.0109 ? 4 HKL-2000 'data reduction' . ? 5 HKL-2000 'data scaling' . ? 6 CCP4 phasing . ? 7 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 G _pdbx_validate_rmsd_angle.auth_seq_id_1 106 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 G _pdbx_validate_rmsd_angle.auth_seq_id_2 106 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N9 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 G _pdbx_validate_rmsd_angle.auth_seq_id_3 106 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 112.79 _pdbx_validate_rmsd_angle.angle_target_value 108.50 _pdbx_validate_rmsd_angle.angle_deviation 4.29 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.70 _pdbx_validate_rmsd_angle.linker_flag N # 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 CFZ P P N N 36 CFZ N1 N N N 37 CFZ C2 C N N 38 CFZ O2 O N N 39 CFZ N3 N N N 40 CFZ C4 C N N 41 CFZ N4 N N N 42 CFZ C5 C N N 43 CFZ C6 C N N 44 CFZ "C1'" C N R 45 CFZ O1P O N N 46 CFZ "C2'" C N R 47 CFZ "F2'" F N N 48 CFZ O2P O N N 49 CFZ "C3'" C N R 50 CFZ "O3'" O N N 51 CFZ O3P O N N 52 CFZ "C4'" C N R 53 CFZ "O4'" O N N 54 CFZ "C5'" C N N 55 CFZ "O5'" O N N 56 CFZ HN4 H N N 57 CFZ HN4A H N N 58 CFZ H5 H N N 59 CFZ H6 H N N 60 CFZ "H1'" H N N 61 CFZ HO1P H N N 62 CFZ "H2'" H N N 63 CFZ "H3'" H N N 64 CFZ "HO3'" H N N 65 CFZ HO3P H N N 66 CFZ "H4'" H N N 67 CFZ "H5'" H N N 68 CFZ "H5'A" H N N 69 G OP3 O N N 70 G P P N N 71 G OP1 O N N 72 G OP2 O N N 73 G "O5'" O N N 74 G "C5'" C N N 75 G "C4'" C N R 76 G "O4'" O N N 77 G "C3'" C N S 78 G "O3'" O N N 79 G "C2'" C N R 80 G "O2'" O N N 81 G "C1'" C N R 82 G N9 N Y N 83 G C8 C Y N 84 G N7 N Y N 85 G C5 C Y N 86 G C6 C N N 87 G O6 O N N 88 G N1 N N N 89 G C2 C N N 90 G N2 N N N 91 G N3 N N N 92 G C4 C Y N 93 G HOP3 H N N 94 G HOP2 H N N 95 G "H5'" H N N 96 G "H5''" H N N 97 G "H4'" H N N 98 G "H3'" H N N 99 G "HO3'" H N N 100 G "H2'" H N N 101 G "HO2'" H N N 102 G "H1'" H N N 103 G H8 H N N 104 G H1 H N N 105 G H21 H N N 106 G H22 H N N 107 GF2 F F N N 108 GF2 P P N N 109 GF2 N1 N N N 110 GF2 C2 C N N 111 GF2 N2 N N N 112 GF2 N3 N N N 113 GF2 C4 C Y N 114 GF2 C5 C Y N 115 GF2 C6 C N N 116 GF2 O6 O N N 117 GF2 N7 N Y N 118 GF2 C8 C Y N 119 GF2 N9 N Y N 120 GF2 "C1'" C N R 121 GF2 OP2 O N N 122 GF2 "C2'" C N R 123 GF2 OP1 O N N 124 GF2 "C3'" C N R 125 GF2 "O3'" O N N 126 GF2 "C4'" C N R 127 GF2 "O4'" O N N 128 GF2 "C5'" C N N 129 GF2 "O5'" O N N 130 GF2 OP3 O N N 131 GF2 HN1 H N N 132 GF2 HN2 H N N 133 GF2 HN2A H N N 134 GF2 H8 H N N 135 GF2 "H1'" H N N 136 GF2 HOP2 H N N 137 GF2 "H2'" H N N 138 GF2 "H3'" H N N 139 GF2 "HO3'" H N N 140 GF2 "H4'" H N N 141 GF2 "H5'" H N N 142 GF2 "H5'A" H N N 143 GF2 HOP3 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 CFZ O2P P doub N N 37 CFZ P "O5'" sing N N 38 CFZ P O1P sing N N 39 CFZ P O3P sing N N 40 CFZ C6 N1 sing N N 41 CFZ C2 N1 sing N N 42 CFZ N1 "C1'" sing N N 43 CFZ N3 C2 sing N N 44 CFZ C2 O2 doub N N 45 CFZ C4 N3 doub N N 46 CFZ N4 C4 sing N N 47 CFZ C4 C5 sing N N 48 CFZ N4 HN4 sing N N 49 CFZ N4 HN4A sing N N 50 CFZ C5 C6 doub N N 51 CFZ C5 H5 sing N N 52 CFZ C6 H6 sing N N 53 CFZ "C2'" "C1'" sing N N 54 CFZ "C1'" "O4'" sing N N 55 CFZ "C1'" "H1'" sing N N 56 CFZ O1P HO1P sing N N 57 CFZ "C3'" "C2'" sing N N 58 CFZ "C2'" "F2'" sing N N 59 CFZ "C2'" "H2'" sing N N 60 CFZ "C3'" "O3'" sing N N 61 CFZ "C3'" "C4'" sing N N 62 CFZ "C3'" "H3'" sing N N 63 CFZ "O3'" "HO3'" sing N N 64 CFZ O3P HO3P sing N N 65 CFZ "O4'" "C4'" sing N N 66 CFZ "C5'" "C4'" sing N N 67 CFZ "C4'" "H4'" sing N N 68 CFZ "O5'" "C5'" sing N N 69 CFZ "C5'" "H5'" sing N N 70 CFZ "C5'" "H5'A" sing N N 71 G OP3 P sing N N 72 G OP3 HOP3 sing N N 73 G P OP1 doub N N 74 G P OP2 sing N N 75 G P "O5'" sing N N 76 G OP2 HOP2 sing N N 77 G "O5'" "C5'" sing N N 78 G "C5'" "C4'" sing N N 79 G "C5'" "H5'" sing N N 80 G "C5'" "H5''" sing N N 81 G "C4'" "O4'" sing N N 82 G "C4'" "C3'" sing N N 83 G "C4'" "H4'" sing N N 84 G "O4'" "C1'" sing N N 85 G "C3'" "O3'" sing N N 86 G "C3'" "C2'" sing N N 87 G "C3'" "H3'" sing N N 88 G "O3'" "HO3'" sing N N 89 G "C2'" "O2'" sing N N 90 G "C2'" "C1'" sing N N 91 G "C2'" "H2'" sing N N 92 G "O2'" "HO2'" sing N N 93 G "C1'" N9 sing N N 94 G "C1'" "H1'" sing N N 95 G N9 C8 sing Y N 96 G N9 C4 sing Y N 97 G C8 N7 doub Y N 98 G C8 H8 sing N N 99 G N7 C5 sing Y N 100 G C5 C6 sing N N 101 G C5 C4 doub Y N 102 G C6 O6 doub N N 103 G C6 N1 sing N N 104 G N1 C2 sing N N 105 G N1 H1 sing N N 106 G C2 N2 sing N N 107 G C2 N3 doub N N 108 G N2 H21 sing N N 109 G N2 H22 sing N N 110 G N3 C4 sing N N 111 GF2 P "O5'" sing N N 112 GF2 N1 C2 sing N N 113 GF2 C2 N3 doub N N 114 GF2 C2 N2 sing N N 115 GF2 C4 N3 sing N N 116 GF2 C5 C4 doub Y N 117 GF2 C6 N1 sing N N 118 GF2 C6 C5 sing N N 119 GF2 O6 C6 doub N N 120 GF2 N7 C5 sing Y N 121 GF2 N7 C8 doub Y N 122 GF2 C8 N9 sing Y N 123 GF2 N9 C4 sing Y N 124 GF2 N9 "C1'" sing N N 125 GF2 "C1'" "O4'" sing N N 126 GF2 OP2 P sing N N 127 GF2 "C2'" F sing N N 128 GF2 "C2'" "C1'" sing N N 129 GF2 OP1 P doub N N 130 GF2 "C3'" "C2'" sing N N 131 GF2 "C3'" "C4'" sing N N 132 GF2 "O3'" "C3'" sing N N 133 GF2 "C4'" "O4'" sing N N 134 GF2 "C5'" "C4'" sing N N 135 GF2 "O5'" "C5'" sing N N 136 GF2 P OP3 sing N N 137 GF2 N1 HN1 sing N N 138 GF2 N2 HN2 sing N N 139 GF2 N2 HN2A sing N N 140 GF2 C8 H8 sing N N 141 GF2 "C1'" "H1'" sing N N 142 GF2 OP2 HOP2 sing N N 143 GF2 "C2'" "H2'" sing N N 144 GF2 "C3'" "H3'" sing N N 145 GF2 "O3'" "HO3'" sing N N 146 GF2 "C4'" "H4'" sing N N 147 GF2 "C5'" "H5'" sing N N 148 GF2 "C5'" "H5'A" sing N N 149 GF2 OP3 HOP3 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _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 1RXB _pdbx_initial_refinement_model.details 'PDB ENTRY 1RXB' #