data_3CJZ # _entry.id 3CJZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 3CJZ pdb_00003cjz 10.2210/pdb3cjz/pdb NDB AR0097 ? ? RCSB RCSB046868 ? ? WWPDB D_1000046868 ? ? # 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 2008-10-14 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2020-07-22 4 'Structure model' 1 3 2024-02-21 5 'Structure model' 1 4 2024-04-03 # _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' Advisory 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 5 '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' ndb_struct_conf_na 2 3 'Structure model' ndb_struct_na_base_pair 3 3 'Structure model' ndb_struct_na_base_pair_step 4 3 'Structure model' pdbx_distant_solvent_atoms 5 3 'Structure model' pdbx_struct_assembly 6 3 'Structure model' pdbx_struct_assembly_gen 7 3 'Structure model' pdbx_struct_assembly_prop 8 3 'Structure model' struct_conn 9 3 'Structure model' struct_ref_seq 10 4 'Structure model' chem_comp_atom 11 4 'Structure model' chem_comp_bond 12 4 'Structure model' database_2 13 5 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_ndb_struct_na_base_pair.buckle' 2 3 'Structure model' '_ndb_struct_na_base_pair.hbond_type_12' 3 3 'Structure model' '_ndb_struct_na_base_pair_step.inclination' 4 3 'Structure model' '_ndb_struct_na_base_pair_step.y_displacement' 5 3 'Structure model' '_pdbx_struct_assembly_prop.value' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 3 'Structure model' '_struct_ref_seq.db_align_beg' 8 3 'Structure model' '_struct_ref_seq.db_align_end' 9 4 'Structure model' '_database_2.pdbx_DOI' 10 4 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3CJZ _pdbx_database_status.recvd_initial_deposition_date 2008-03-14 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _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 'Kreutz, C.' 2 'Bosio, S.' 3 'Micura, R.' 4 'Egli, M.' 5 # _citation.id primary _citation.title 'Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs.' _citation.journal_abbrev Rna _citation.journal_volume 14 _citation.page_first 2125 _citation.page_last 2135 _citation.year 2008 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18772248 _citation.pdbx_database_id_DOI 10.1261/rna.1078508 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pallan, P.S.' 1 ? primary 'Kreutz, C.' 2 ? primary 'Bosio, S.' 3 ? primary 'Micura, R.' 4 ? primary 'Egli, M.' 5 ? # 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 (5'-R(*GP*GP*AP*CP*GP*(M2G)P*AP*CP*GP*UP*CP*CP*U)-3') ; 4200.595 2 ? ? ? ? 2 water nat water 18.015 115 ? ? ? ? # _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 'GGACG(M2G)ACGUCCU' _entity_poly.pdbx_seq_one_letter_code_can GGACGGACGUCCU _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 A n 1 4 C n 1 5 G n 1 6 M2G n 1 7 A n 1 8 C n 1 9 G n 1 10 U n 1 11 C n 1 12 C n 1 13 U n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 M2G 'RNA linking' n "N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE" ? 'C12 H18 N5 O8 P' 391.274 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 M2G 6 6 6 M2G M2G A . n A 1 7 A 7 7 7 A A A . n A 1 8 C 8 8 8 C C A . n A 1 9 G 9 9 9 G G A . n A 1 10 U 10 10 10 U U A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 U 13 13 13 U U A . n B 1 1 G 1 14 14 G G B . n B 1 2 G 2 15 15 G G B . n B 1 3 A 3 16 16 A A B . n B 1 4 C 4 17 17 C C B . n B 1 5 G 5 18 18 G G B . n B 1 6 M2G 6 19 19 M2G M2G B . n B 1 7 A 7 20 20 A A B . n B 1 8 C 8 21 21 C C B . n B 1 9 G 9 22 22 G G B . n B 1 10 U 10 23 23 U U B . n B 1 11 C 11 24 24 C C B . n B 1 12 C 12 25 25 C C B . n B 1 13 U 13 26 26 U U 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 1 102 102 HOH HOH A . C 2 HOH 2 103 103 HOH HOH A . C 2 HOH 3 104 104 HOH HOH A . C 2 HOH 4 107 107 HOH HOH A . C 2 HOH 5 112 112 HOH HOH A . C 2 HOH 6 114 114 HOH HOH A . C 2 HOH 7 116 116 HOH HOH A . C 2 HOH 8 121 121 HOH HOH A . C 2 HOH 9 125 125 HOH HOH A . C 2 HOH 10 126 126 HOH HOH A . C 2 HOH 11 127 127 HOH HOH A . C 2 HOH 12 134 134 HOH HOH A . C 2 HOH 13 136 136 HOH HOH A . C 2 HOH 14 140 140 HOH HOH A . C 2 HOH 15 144 144 HOH HOH A . C 2 HOH 16 148 148 HOH HOH A . C 2 HOH 17 151 151 HOH HOH A . C 2 HOH 18 152 152 HOH HOH A . C 2 HOH 19 154 154 HOH HOH A . C 2 HOH 20 156 156 HOH HOH A . C 2 HOH 21 161 161 HOH HOH A . C 2 HOH 22 169 169 HOH HOH A . C 2 HOH 23 171 171 HOH HOH A . C 2 HOH 24 173 173 HOH HOH A . C 2 HOH 25 179 179 HOH HOH A . C 2 HOH 26 180 180 HOH HOH A . C 2 HOH 27 181 181 HOH HOH A . C 2 HOH 28 183 183 HOH HOH A . C 2 HOH 29 189 189 HOH HOH A . C 2 HOH 30 190 190 HOH HOH A . C 2 HOH 31 191 191 HOH HOH A . C 2 HOH 32 192 192 HOH HOH A . C 2 HOH 33 193 193 HOH HOH A . C 2 HOH 34 194 194 HOH HOH A . C 2 HOH 35 196 196 HOH HOH A . C 2 HOH 36 198 198 HOH HOH A . C 2 HOH 37 199 199 HOH HOH A . C 2 HOH 38 202 202 HOH HOH A . C 2 HOH 39 211 211 HOH HOH A . C 2 HOH 40 212 212 HOH HOH A . C 2 HOH 41 215 215 HOH HOH A . C 2 HOH 42 218 218 HOH HOH A . C 2 HOH 43 219 219 HOH HOH A . C 2 HOH 44 221 221 HOH HOH A . C 2 HOH 45 224 224 HOH HOH A . C 2 HOH 46 229 229 HOH HOH A . C 2 HOH 47 234 234 HOH HOH A . C 2 HOH 48 235 235 HOH HOH A . C 2 HOH 49 236 236 HOH HOH A . C 2 HOH 50 238 238 HOH HOH A . D 2 HOH 1 101 101 HOH HOH B . D 2 HOH 2 105 105 HOH HOH B . D 2 HOH 3 106 106 HOH HOH B . D 2 HOH 4 108 108 HOH HOH B . D 2 HOH 5 109 109 HOH HOH B . D 2 HOH 6 110 110 HOH HOH B . D 2 HOH 7 111 111 HOH HOH B . D 2 HOH 8 113 113 HOH HOH B . D 2 HOH 9 115 115 HOH HOH B . D 2 HOH 10 117 117 HOH HOH B . D 2 HOH 11 118 118 HOH HOH B . D 2 HOH 12 119 119 HOH HOH B . D 2 HOH 13 120 120 HOH HOH B . D 2 HOH 14 122 122 HOH HOH B . D 2 HOH 15 123 123 HOH HOH B . D 2 HOH 16 124 124 HOH HOH B . D 2 HOH 17 129 129 HOH HOH B . D 2 HOH 18 130 130 HOH HOH B . D 2 HOH 19 131 131 HOH HOH B . D 2 HOH 20 132 132 HOH HOH B . D 2 HOH 21 133 133 HOH HOH B . D 2 HOH 22 135 135 HOH HOH B . D 2 HOH 23 137 137 HOH HOH B . D 2 HOH 24 138 138 HOH HOH B . D 2 HOH 25 139 139 HOH HOH B . D 2 HOH 26 141 141 HOH HOH B . D 2 HOH 27 145 145 HOH HOH B . D 2 HOH 28 149 149 HOH HOH B . D 2 HOH 29 153 153 HOH HOH B . D 2 HOH 30 155 155 HOH HOH B . D 2 HOH 31 158 158 HOH HOH B . D 2 HOH 32 159 159 HOH HOH B . D 2 HOH 33 160 160 HOH HOH B . D 2 HOH 34 162 162 HOH HOH B . D 2 HOH 35 163 163 HOH HOH B . D 2 HOH 36 164 164 HOH HOH B . D 2 HOH 37 166 166 HOH HOH B . D 2 HOH 38 168 168 HOH HOH B . D 2 HOH 39 170 170 HOH HOH B . D 2 HOH 40 172 172 HOH HOH B . D 2 HOH 41 177 177 HOH HOH B . D 2 HOH 42 184 184 HOH HOH B . D 2 HOH 43 186 186 HOH HOH B . D 2 HOH 44 187 187 HOH HOH B . D 2 HOH 45 188 188 HOH HOH B . D 2 HOH 46 203 203 HOH HOH B . D 2 HOH 47 204 204 HOH HOH B . D 2 HOH 48 205 205 HOH HOH B . D 2 HOH 49 207 207 HOH HOH B . D 2 HOH 50 208 208 HOH HOH B . D 2 HOH 51 209 209 HOH HOH B . D 2 HOH 52 210 210 HOH HOH B . D 2 HOH 53 213 213 HOH HOH B . D 2 HOH 54 217 217 HOH HOH B . D 2 HOH 55 222 222 HOH HOH B . D 2 HOH 56 223 223 HOH HOH B . D 2 HOH 57 226 226 HOH HOH B . D 2 HOH 58 230 230 HOH HOH B . D 2 HOH 59 232 232 HOH HOH B . D 2 HOH 60 233 233 HOH HOH B . D 2 HOH 61 239 239 HOH HOH B . D 2 HOH 62 241 241 HOH HOH B . D 2 HOH 63 242 242 HOH HOH B . D 2 HOH 64 243 243 HOH HOH B . D 2 HOH 65 244 244 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0003 ? 1 HKL-2000 'data collection' . ? 2 X-GEN 'data reduction' . ? 3 X-GEN 'data scaling' . ? 4 MOLREP phasing '(CCP4)' ? 5 # _cell.entry_id 3CJZ _cell.length_a 58.118 _cell.length_b 25.970 _cell.length_c 45.393 _cell.angle_alpha 90.00 _cell.angle_beta 97.41 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 3CJZ _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3CJZ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.02 _exptl_crystal.density_percent_sol 39.16 _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 301 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;2ul droplets containing 0.5mM oligonucleotide, 5% 2-methyl -2,4-pentanediol (MPD), 20mM sodium cacodylate, pH 7.0, 6mM spermine-4HCl, 40mM sodium chloride that were equilibrated against a reservoir of 1ml of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 301K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 '5% MPD' ? ? ? 1 2 1 'sodium cacodylate' ? ? ? 1 3 1 spermine-4HCl ? ? ? 1 4 1 'sodium chloride' ? ? ? 1 5 2 '35% MPD' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 120 _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 2004-11-09 _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 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 22-BM' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 22-BM _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.entry_id 3CJZ _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 1.80 _reflns.d_resolution_low 44.99 _reflns.number_all 6420 _reflns.number_obs 6027 _reflns.percent_possible_obs 93.9 _reflns.pdbx_Rmerge_I_obs 0.099 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 26.4 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 2.0 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.80 _reflns_shell.d_res_low 1.86 _reflns_shell.percent_possible_all 81.4 _reflns_shell.Rmerge_I_obs 0.3539 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.8 _reflns_shell.pdbx_redundancy 1.9 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 661 _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 3CJZ _refine.ls_number_reflns_obs 4816 _refine.ls_number_reflns_all 6420 _refine.pdbx_ls_sigma_I 0 _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 44.99 _refine.ls_d_res_high 1.80 _refine.ls_percent_reflns_obs 84.12 _refine.ls_R_factor_obs 0.19938 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.19005 _refine.ls_R_factor_R_free 0.27742 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.8 _refine.ls_number_reflns_R_free 582 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.960 _refine.correlation_coeff_Fo_to_Fc_free 0.927 _refine.B_iso_mean 25.807 _refine.aniso_B[1][1] -1.88 _refine.aniso_B[2][2] 0.18 _refine.aniso_B[3][3] 1.86 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.63 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'A cononical A-RNA dodecamer generated with the program TURBO-FRODO omitting U13 and U26.' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Anisotropic _refine.pdbx_stereochemistry_target_values ;Standard Refmac parameters and the parameters generated by PRODRG (Schuettelkopf, A. W. and van Aalten, D.M.F. 2004. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr. D Biol. Crystallogr. 60: 1355-1363.) for the residue M2G. ; _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 0.210 _refine.overall_SU_ML 0.135 _refine.overall_SU_B 9.576 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _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_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 556 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 115 _refine_hist.number_atoms_total 671 _refine_hist.d_res_high 1.80 _refine_hist.d_res_low 44.99 # 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 0.008 0.021 ? 620 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 222 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.356 3.007 ? 948 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.124 3.000 ? 576 'X-RAY DIFFRACTION' ? r_chiral_restr 0.051 0.200 ? 126 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.020 ? 276 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.004 0.020 ? 2 'X-RAY DIFFRACTION' ? r_nbd_refined 0.108 0.200 ? 76 'X-RAY DIFFRACTION' ? r_nbd_other 0.249 0.200 ? 276 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.236 0.200 ? 230 'X-RAY DIFFRACTION' ? r_nbtor_other 0.077 0.200 ? 128 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.146 0.200 ? 85 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other 0.075 0.200 ? 2 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.084 0.200 ? 14 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.212 0.200 ? 27 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.154 0.200 ? 28 'X-RAY DIFFRACTION' ? r_scbond_it 1.582 3.000 ? 931 'X-RAY DIFFRACTION' ? r_scangle_it 1.993 4.500 ? 948 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.80 _refine_ls_shell.d_res_low 1.847 _refine_ls_shell.number_reflns_R_work 235 _refine_ls_shell.R_factor_R_work 0.209 _refine_ls_shell.percent_reflns_obs 56.16 _refine_ls_shell.R_factor_R_free 0.248 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 25 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 235 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3CJZ _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 3CJZ _struct.title 'Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m22G:A pairs' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3CJZ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, N2, N2-dimethyl guanosine, X-ray crystal structure, m22G:A pair, rRNA, tRNA' # 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_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3CJZ _struct_ref.pdbx_db_accession 3CJZ _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GGACGGACGUCCU _struct_ref.pdbx_align_begin 1 _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 3CJZ A 1 ? 13 ? 3CJZ 1 ? 13 ? 1 13 2 1 3CJZ B 1 ? 13 ? 3CJZ 14 ? 26 ? 14 26 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2460 ? 1 MORE 1 ? 1 'SSA (A^2)' 4790 ? # _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_ _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 G 5 "O3'" ? ? ? 1_555 A M2G 6 P ? ? A G 5 A M2G 6 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A M2G 6 "O3'" ? ? ? 1_555 A A 7 P ? ? A M2G 6 A A 7 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale3 covale both ? B G 5 "O3'" ? ? ? 1_555 B M2G 6 P ? ? B G 18 B M2G 19 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale4 covale both ? B M2G 6 "O3'" ? ? ? 1_555 B A 7 P ? ? B M2G 19 B A 20 1_555 ? ? ? ? ? ? ? 1.585 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 2 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 2 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 2 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 3 B U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 3 B U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 4 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 4 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 4 B G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 5 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 5 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 5 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A M2G 6 N1 ? ? ? 1_555 B A 7 N1 ? ? A M2G 6 B A 20 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog16 hydrog ? ? A M2G 6 O6 ? ? ? 1_555 B A 7 N6 ? ? A M2G 6 B A 20 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog17 hydrog ? ? A A 7 N1 ? ? ? 1_555 B M2G 6 N1 ? ? A A 7 B M2G 19 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog18 hydrog ? ? A A 7 N6 ? ? ? 1_555 B M2G 6 O6 ? ? A A 7 B M2G 19 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog19 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 8 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 8 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 8 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 9 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 9 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 9 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 10 B A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 10 B A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 11 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 11 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 12 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 12 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 12 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A C 4 ? ? "C1'" A C 4 ? ? N1 A C 4 ? ? 112.86 108.50 4.36 0.70 N 2 1 "O3'" A G 5 ? ? P A M2G 6 ? ? OP2 A M2G 6 ? ? 118.06 110.50 7.56 1.10 Y # 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 M2G 6 A M2G 6 ? G "N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE" 2 B M2G 6 B M2G 19 ? G "N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE" # 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 171 ? C HOH . 2 1 B HOH 243 ? D HOH . # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 0.1389 _pdbx_refine_tls.origin_y -1.8722 _pdbx_refine_tls.origin_z 10.7909 _pdbx_refine_tls.T[1][1] -0.0232 _pdbx_refine_tls.T[2][2] -0.0549 _pdbx_refine_tls.T[3][3] -0.0589 _pdbx_refine_tls.T[1][2] 0.0022 _pdbx_refine_tls.T[1][3] 0.0009 _pdbx_refine_tls.T[2][3] -0.0114 _pdbx_refine_tls.L[1][1] 2.0857 _pdbx_refine_tls.L[2][2] 0.2961 _pdbx_refine_tls.L[3][3] 0.6885 _pdbx_refine_tls.L[1][2] -0.3434 _pdbx_refine_tls.L[1][3] 0.2795 _pdbx_refine_tls.L[2][3] -0.2948 _pdbx_refine_tls.S[1][1] -0.0909 _pdbx_refine_tls.S[1][2] 0.0157 _pdbx_refine_tls.S[1][3] -0.0475 _pdbx_refine_tls.S[2][1] 0.0225 _pdbx_refine_tls.S[2][2] 0.0412 _pdbx_refine_tls.S[2][3] -0.0166 _pdbx_refine_tls.S[3][1] -0.0058 _pdbx_refine_tls.S[3][2] 0.0232 _pdbx_refine_tls.S[3][3] 0.0496 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _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.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 A 1 A 1 A 13 A 13 ? 'X-RAY DIFFRACTION' ? 2 1 B 14 B 1 B 26 B 13 ? 'X-RAY DIFFRACTION' ? # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 112 ? 5.94 . 2 1 O ? A HOH 238 ? 7.01 . 3 1 O ? B HOH 166 ? 6.85 . 4 1 O ? B HOH 230 ? 6.20 . 5 1 O ? B HOH 233 ? 6.18 . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 M2G P P N N 114 M2G OP1 O N N 115 M2G OP2 O N N 116 M2G OP3 O N N 117 M2G "O5'" O N N 118 M2G "C5'" C N N 119 M2G "C4'" C N R 120 M2G "O4'" O N N 121 M2G "C3'" C N S 122 M2G "O3'" O N N 123 M2G "C2'" C N R 124 M2G "O2'" O N N 125 M2G "C1'" C N R 126 M2G N9 N Y N 127 M2G C8 C Y N 128 M2G N7 N Y N 129 M2G C5 C Y N 130 M2G C6 C N N 131 M2G O6 O N N 132 M2G N1 N N N 133 M2G C2 C N N 134 M2G N2 N N N 135 M2G N3 N N N 136 M2G C4 C Y N 137 M2G CM1 C N N 138 M2G CM2 C N N 139 M2G HOP2 H N N 140 M2G HOP3 H N N 141 M2G "H5'" H N N 142 M2G "H5''" H N N 143 M2G "H4'" H N N 144 M2G "H3'" H N N 145 M2G "HO3'" H N N 146 M2G "H2'" H N N 147 M2G "HO2'" H N N 148 M2G "H1'" H N N 149 M2G H8 H N N 150 M2G HN1 H N N 151 M2G HM11 H N N 152 M2G HM12 H N N 153 M2G HM13 H N N 154 M2G HM21 H N N 155 M2G HM22 H N N 156 M2G HM23 H N N 157 U OP3 O N N 158 U P P N N 159 U OP1 O N N 160 U OP2 O N N 161 U "O5'" O N N 162 U "C5'" C N N 163 U "C4'" C N R 164 U "O4'" O N N 165 U "C3'" C N S 166 U "O3'" O N N 167 U "C2'" C N R 168 U "O2'" O N N 169 U "C1'" C N R 170 U N1 N N N 171 U C2 C N N 172 U O2 O N N 173 U N3 N N N 174 U C4 C N N 175 U O4 O N N 176 U C5 C N N 177 U C6 C N N 178 U HOP3 H N N 179 U HOP2 H N N 180 U "H5'" H N N 181 U "H5''" H N N 182 U "H4'" H N N 183 U "H3'" H N N 184 U "HO3'" H N N 185 U "H2'" H N N 186 U "HO2'" H N N 187 U "H1'" H N N 188 U H3 H N N 189 U H5 H N N 190 U H6 H N N 191 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 M2G P OP1 doub N N 118 M2G P OP2 sing N N 119 M2G P OP3 sing N N 120 M2G P "O5'" sing N N 121 M2G OP2 HOP2 sing N N 122 M2G OP3 HOP3 sing N N 123 M2G "O5'" "C5'" sing N N 124 M2G "C5'" "C4'" sing N N 125 M2G "C5'" "H5'" sing N N 126 M2G "C5'" "H5''" sing N N 127 M2G "C4'" "O4'" sing N N 128 M2G "C4'" "C3'" sing N N 129 M2G "C4'" "H4'" sing N N 130 M2G "O4'" "C1'" sing N N 131 M2G "C3'" "O3'" sing N N 132 M2G "C3'" "C2'" sing N N 133 M2G "C3'" "H3'" sing N N 134 M2G "O3'" "HO3'" sing N N 135 M2G "C2'" "O2'" sing N N 136 M2G "C2'" "C1'" sing N N 137 M2G "C2'" "H2'" sing N N 138 M2G "O2'" "HO2'" sing N N 139 M2G "C1'" N9 sing N N 140 M2G "C1'" "H1'" sing N N 141 M2G N9 C8 sing Y N 142 M2G N9 C4 sing Y N 143 M2G C8 N7 doub Y N 144 M2G C8 H8 sing N N 145 M2G N7 C5 sing Y N 146 M2G C5 C6 sing N N 147 M2G C5 C4 doub Y N 148 M2G C6 O6 doub N N 149 M2G C6 N1 sing N N 150 M2G N1 C2 sing N N 151 M2G N1 HN1 sing N N 152 M2G C2 N2 sing N N 153 M2G C2 N3 doub N N 154 M2G N2 CM1 sing N N 155 M2G N2 CM2 sing N N 156 M2G N3 C4 sing N N 157 M2G CM1 HM11 sing N N 158 M2G CM1 HM12 sing N N 159 M2G CM1 HM13 sing N N 160 M2G CM2 HM21 sing N N 161 M2G CM2 HM22 sing N N 162 M2G CM2 HM23 sing N N 163 U OP3 P sing N N 164 U OP3 HOP3 sing N N 165 U P OP1 doub N N 166 U P OP2 sing N N 167 U P "O5'" sing N N 168 U OP2 HOP2 sing N N 169 U "O5'" "C5'" sing N N 170 U "C5'" "C4'" sing N N 171 U "C5'" "H5'" sing N N 172 U "C5'" "H5''" sing N N 173 U "C4'" "O4'" sing N N 174 U "C4'" "C3'" sing N N 175 U "C4'" "H4'" sing N N 176 U "O4'" "C1'" sing N N 177 U "C3'" "O3'" sing N N 178 U "C3'" "C2'" sing N N 179 U "C3'" "H3'" sing N N 180 U "O3'" "HO3'" sing N N 181 U "C2'" "O2'" sing N N 182 U "C2'" "C1'" sing N N 183 U "C2'" "H2'" sing N N 184 U "O2'" "HO2'" sing N N 185 U "C1'" N1 sing N N 186 U "C1'" "H1'" sing N N 187 U N1 C2 sing N N 188 U N1 C6 sing N N 189 U C2 O2 doub N N 190 U C2 N3 sing N N 191 U N3 C4 sing N N 192 U N3 H3 sing N N 193 U C4 O4 doub N N 194 U C4 C5 sing N N 195 U C5 C6 doub N N 196 U C5 H5 sing N N 197 U C6 H6 sing N N 198 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3CJZ 'double helix' 3CJZ 'a-form double helix' # 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 G 1 1_555 B C 12 1_555 -0.322 -0.392 0.047 -1.404 -3.333 -2.552 1 A_G1:C25_B A 1 ? B 25 ? 19 1 1 A G 2 1_555 B C 11 1_555 -0.099 -0.292 0.100 -1.918 -14.752 -1.850 2 A_G2:C24_B A 2 ? B 24 ? 19 1 1 A A 3 1_555 B U 10 1_555 -0.200 -0.233 0.066 -7.788 -15.409 -4.850 3 A_A3:U23_B A 3 ? B 23 ? 20 1 1 A C 4 1_555 B G 9 1_555 0.359 -0.166 0.272 -1.327 -17.459 1.514 4 A_C4:G22_B A 4 ? B 22 ? 19 1 1 A G 5 1_555 B C 8 1_555 -0.123 -0.219 -0.074 -7.320 -19.634 -3.478 5 A_G5:C21_B A 5 ? B 21 ? 19 1 1 A M2G 6 1_555 B A 7 1_555 -0.382 1.729 -0.230 4.240 -1.812 -35.019 6 A_M2G6:A20_B A 6 ? B 20 ? 8 1 1 A A 7 1_555 B M2G 6 1_555 0.212 1.683 -0.248 3.995 -15.961 -28.730 7 A_A7:M2G19_B A 7 ? B 19 ? 8 1 1 A C 8 1_555 B G 5 1_555 0.427 -0.159 0.030 13.245 -22.031 -0.800 8 A_C8:G18_B A 8 ? B 18 ? 19 1 1 A G 9 1_555 B C 4 1_555 -0.569 -0.219 -0.047 -2.993 -21.441 1.034 9 A_G9:C17_B A 9 ? B 17 ? 19 1 1 A U 10 1_555 B A 3 1_555 -0.171 -0.162 0.040 -1.165 -14.732 -1.396 10 A_U10:A16_B A 10 ? B 16 ? 20 1 1 A C 11 1_555 B G 2 1_555 0.274 -0.320 0.213 0.615 -15.513 -1.081 11 A_C11:G15_B A 11 ? B 15 ? 19 1 1 A C 12 1_555 B G 1 1_555 0.373 -0.286 0.111 2.009 -10.878 -0.763 12 A_C12:G14_B A 12 ? B 14 ? 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 G 1 1_555 B C 12 1_555 A G 2 1_555 B C 11 1_555 0.189 -1.746 3.214 0.401 8.484 32.703 -4.268 -0.266 2.692 14.759 -0.698 33.759 1 AA_G1G2:C24C25_BB A 1 ? B 25 ? A 2 ? B 24 ? 1 A G 2 1_555 B C 11 1_555 A A 3 1_555 B U 10 1_555 -0.332 -1.501 3.353 0.803 3.751 35.758 -2.967 0.653 3.176 6.087 -1.303 35.957 2 AA_G2A3:U23C24_BB A 2 ? B 24 ? A 3 ? B 23 ? 1 A A 3 1_555 B U 10 1_555 A C 4 1_555 B G 9 1_555 0.690 -1.219 3.011 1.008 5.893 33.034 -2.974 -1.047 2.778 10.259 -1.755 33.556 3 AA_A3C4:G22U23_BB A 3 ? B 23 ? A 4 ? B 22 ? 1 A C 4 1_555 B G 9 1_555 A G 5 1_555 B C 8 1_555 -0.205 -1.694 3.196 4.176 15.463 31.462 -4.782 0.874 2.116 26.478 -7.150 35.213 4 AA_C4G5:C21G22_BB A 4 ? B 22 ? A 5 ? B 21 ? 1 A G 5 1_555 B C 8 1_555 A M2G 6 1_555 B A 7 1_555 -1.827 -1.109 3.012 -0.145 12.599 30.124 -3.859 3.234 2.378 23.015 0.265 32.597 5 AA_G5M2G6:A20C21_BB A 5 ? B 21 ? A 6 ? B 20 ? 1 A M2G 6 1_555 B A 7 1_555 A A 7 1_555 B M2G 6 1_555 0.734 -1.900 3.256 0.803 8.798 31.539 -4.774 -1.175 2.660 15.801 -1.442 32.723 6 AA_M2G6A7:M2G19A20_BB A 6 ? B 20 ? A 7 ? B 19 ? 1 A A 7 1_555 B M2G 6 1_555 A C 8 1_555 B G 5 1_555 1.589 -1.231 2.933 0.841 10.272 30.081 -3.839 -2.773 2.434 19.100 -1.564 31.759 7 AA_A7C8:G18M2G19_BB A 7 ? B 19 ? A 8 ? B 18 ? 1 A C 8 1_555 B G 5 1_555 A G 9 1_555 B C 4 1_555 -0.028 -1.290 3.496 -1.853 16.153 33.980 -4.086 -0.195 2.636 25.883 2.969 37.566 8 AA_C8G9:C17G18_BB A 8 ? B 18 ? A 9 ? B 17 ? 1 A G 9 1_555 B C 4 1_555 A U 10 1_555 B A 3 1_555 -0.454 -1.067 3.112 -2.975 9.154 32.920 -3.129 0.343 2.755 15.739 5.115 34.261 9 AA_G9U10:A16C17_BB A 9 ? B 17 ? A 10 ? B 16 ? 1 A U 10 1_555 B A 3 1_555 A C 11 1_555 B G 2 1_555 0.492 -1.221 3.175 -0.074 4.225 34.626 -2.645 -0.832 3.009 7.066 0.124 34.875 10 AA_U10C11:G15A16_BB A 10 ? B 16 ? A 11 ? B 15 ? 1 A C 11 1_555 B G 2 1_555 A C 12 1_555 B G 1 1_555 -0.119 -1.687 3.167 0.547 5.380 33.956 -3.636 0.281 2.872 9.139 -0.929 34.372 11 AA_C11C12:G14G15_BB A 11 ? B 15 ? A 12 ? B 14 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'canonical A-form RNA dodecamer omitting U13 and U26' # _atom_sites.entry_id 3CJZ _atom_sites.fract_transf_matrix[1][1] 0.017206 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.002238 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.038506 _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] 0.022215 _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 N O P # loop_