data_1VRO # _entry.id 1VRO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 1VRO pdb_00001vro 10.2210/pdb1vro/pdb NDB ZD0015 ? ? RCSB RCSB002092 ? ? WWPDB D_1000002092 ? ? # 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 2005-04-19 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-07-24 5 'Structure model' 1 4 2023-12-27 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Refinement description' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' 8 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 4 'Structure model' struct_conn 3 5 'Structure model' chem_comp_atom 4 5 'Structure model' chem_comp_bond 5 5 'Structure model' database_2 6 5 'Structure model' pdbx_struct_conn_angle 7 5 'Structure model' struct_conn 8 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.value' 19 5 'Structure model' '_struct_conn.pdbx_dist_value' 20 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 21 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 25 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 26 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 32 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2005-04-19 _pdbx_database_PDB_obs_spr.pdb_id 1vro _pdbx_database_PDB_obs_spr.replace_pdb_id 1n6s _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1VRO _pdbx_database_status.recvd_initial_deposition_date 2005-04-14 _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wilds, C.J.' 1 'Pattanayek, R.' 2 'Pan, C.' 3 'Wawrzak, Z.' 4 'Egli, M.' 5 # _citation.id primary _citation.title 'Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 124 _citation.page_first 14910 _citation.page_last 14916 _citation.year 2002 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12475332 _citation.pdbx_database_id_DOI 10.1021/ja021058b # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wilds, C.J.' 1 ? primary 'Pattanayek, R.' 2 ? primary 'Pan, C.' 3 ? primary 'Wawrzak, Z.' 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 "5'-D(*CP*(GMS)P*CP*GP*CP*G)-3'" 1873.166 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 73 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(GMS)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMINE SPM 3 'MAGNESIUM ION' MG 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 GMS n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 DG 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 ;synthesized with a solid-phase oligonucleotide synthesizer using DNA phosphoramidites and potassium selenocyanide for introducing the phosphoroselenoate linkage ; # 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 GMS 'DNA linking' n "2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE" ? 'C10 H14 N5 O6 P Se' 410.182 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # 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 DC 1 1 1 DC C A . n A 1 2 GMS 2 2 2 GMS GMS A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n B 1 1 DC 1 107 107 DC C B . n B 1 2 GMS 2 108 108 GMS GMS B . n B 1 3 DC 3 109 109 DC C B . n B 1 4 DG 4 110 110 DG G B . n B 1 5 DC 5 111 111 DC C B . n B 1 6 DG 6 112 112 DG 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 SPM 1 201 201 SPM SPM A . D 3 MG 1 301 301 MG MG B . E 4 HOH 1 401 401 HOH HOH A . E 4 HOH 2 402 402 HOH HOH A . E 4 HOH 3 405 405 HOH HOH A . E 4 HOH 4 406 406 HOH HOH A . E 4 HOH 5 407 407 HOH HOH A . E 4 HOH 6 408 408 HOH HOH A . E 4 HOH 7 410 410 HOH HOH A . E 4 HOH 8 411 411 HOH HOH A . E 4 HOH 9 415 415 HOH HOH A . E 4 HOH 10 416 416 HOH HOH A . E 4 HOH 11 417 417 HOH HOH A . E 4 HOH 12 419 419 HOH HOH A . E 4 HOH 13 424 424 HOH HOH A . E 4 HOH 14 426 426 HOH HOH A . E 4 HOH 15 430 430 HOH HOH A . E 4 HOH 16 432 432 HOH HOH A . E 4 HOH 17 433 433 HOH HOH A . E 4 HOH 18 436 436 HOH HOH A . E 4 HOH 19 438 438 HOH HOH A . E 4 HOH 20 441 441 HOH HOH A . E 4 HOH 21 442 442 HOH HOH A . E 4 HOH 22 443 443 HOH HOH A . E 4 HOH 23 446 446 HOH HOH A . E 4 HOH 24 447 447 HOH HOH A . E 4 HOH 25 450 450 HOH HOH A . E 4 HOH 26 451 451 HOH HOH A . E 4 HOH 27 453 453 HOH HOH A . E 4 HOH 28 454 454 HOH HOH A . E 4 HOH 29 455 455 HOH HOH A . E 4 HOH 30 457 457 HOH HOH A . E 4 HOH 31 458 458 HOH HOH A . E 4 HOH 32 459 459 HOH HOH A . E 4 HOH 33 460 460 HOH HOH A . E 4 HOH 34 461 461 HOH HOH A . E 4 HOH 35 463 463 HOH HOH A . E 4 HOH 36 464 464 HOH HOH A . E 4 HOH 37 469 469 HOH HOH A . F 4 HOH 1 403 403 HOH HOH B . F 4 HOH 2 404 404 HOH HOH B . F 4 HOH 3 409 409 HOH HOH B . F 4 HOH 4 412 412 HOH HOH B . F 4 HOH 5 413 413 HOH HOH B . F 4 HOH 6 414 414 HOH HOH B . F 4 HOH 7 418 418 HOH HOH B . F 4 HOH 8 420 420 HOH HOH B . F 4 HOH 9 421 421 HOH HOH B . F 4 HOH 10 422 422 HOH HOH B . F 4 HOH 11 423 423 HOH HOH B . F 4 HOH 12 425 425 HOH HOH B . F 4 HOH 13 427 427 HOH HOH B . F 4 HOH 14 428 428 HOH HOH B . F 4 HOH 15 429 429 HOH HOH B . F 4 HOH 16 431 431 HOH HOH B . F 4 HOH 17 434 434 HOH HOH B . F 4 HOH 18 435 435 HOH HOH B . F 4 HOH 19 437 437 HOH HOH B . F 4 HOH 20 439 439 HOH HOH B . F 4 HOH 21 440 440 HOH HOH B . F 4 HOH 22 444 444 HOH HOH B . F 4 HOH 23 445 445 HOH HOH B . F 4 HOH 24 448 448 HOH HOH B . F 4 HOH 25 449 449 HOH HOH B . F 4 HOH 26 452 452 HOH HOH B . F 4 HOH 27 456 456 HOH HOH B . F 4 HOH 28 462 462 HOH HOH B . F 4 HOH 29 465 465 HOH HOH B . F 4 HOH 30 466 466 HOH HOH B . F 4 HOH 31 467 467 HOH HOH B . F 4 HOH 32 468 468 HOH HOH B . F 4 HOH 33 470 470 HOH HOH B . F 4 HOH 34 471 471 HOH HOH B . F 4 HOH 35 472 472 HOH HOH B . F 4 HOH 36 473 473 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-97 refinement . ? 1 SCALEPACK 'data scaling' . ? 2 CNS refinement . ? 3 DENZO 'data reduction' . ? 4 CNS phasing . ? 5 # _cell.entry_id 1VRO _cell.length_a 17.778 _cell.length_b 31.348 _cell.length_c 44.116 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 # _symmetry.entry_id 1VRO _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 19 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.entry_id 1VRO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.32 _exptl_crystal.density_percent_sol 5.98 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 291.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;0.5mM DNA, 4mM-15mM magnesium chloride, 50mM sodium cacodylate, 2mM-8mM spermine tetrahydrochloride and reservoir 30% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K ; _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 DNA ? ? ? 1 2 1 MgCl ? ? ? 1 3 1 'sodium cacodylate' ? ? ? 1 4 1 'spermine tetrahydrochloride' ? ? ? 1 5 2 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 MARRESEARCH _diffrn_detector.pdbx_collection_date 2002-01-22 _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 graphite _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9561 1.0 2 0.9787 1.0 3 0.9784 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 5ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 5ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9561, 0.9787, 0.9784' # _reflns.entry_id 1VRO _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 1.1 _reflns.d_resolution_low 20.0 _reflns.number_all 10197 _reflns.number_obs 9718 _reflns.percent_possible_obs 97.7 _reflns.pdbx_Rmerge_I_obs 0.041 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 22.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.47 _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 1.10 _reflns_shell.d_res_low 1.14 _reflns_shell.percent_possible_all 95.4 _reflns_shell.Rmerge_I_obs 0.075 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 15.85 _reflns_shell.pdbx_redundancy 7.47 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1802 _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 1VRO _refine.ls_d_res_high 1.10 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I 0.0 _refine.ls_number_reflns_all 9718 _refine.ls_number_reflns_obs 9718 _refine.ls_number_reflns_R_free 508 _refine.ls_percent_reflns_obs 97.7 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.097 _refine.ls_R_factor_R_free 0.129 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters 3005 _refine.ls_number_restraints 5144 _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean 6.9 _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.details Shelx-97 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 245 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 73 _refine_hist.number_atoms_total 333 _refine_hist.d_res_high 1.10 _refine_hist.d_res_low 20.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.028 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.022 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1VRO _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.097 _pdbx_refine.number_reflns_obs_no_cutoff 9718 _pdbx_refine.free_R_factor_no_cutoff 0.129 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 508 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff 0.096 _pdbx_refine.number_reflns_obs_4sig_cutoff 9692 _pdbx_refine.free_R_factor_4sig_cutoff 0.129 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 508 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1VRO _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 1VRO _struct.title 'Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1VRO _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;Left-handed Z-DNA, phosphoroselenoate, multiwavelength anomalous dispersion (MAD), covalent modification of oligonucleotides, oligonucleotide analogue, phasing strategy, synchrotron, DNA ; # 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 3 ? E N N 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1VRO _struct_ref.pdbx_db_accession 1VRO _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1VRO A 1 ? 6 ? 1VRO 1 ? 6 ? 1 6 2 1 1VRO B 1 ? 6 ? 1VRO 107 ? 112 ? 107 112 # _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,E,F # _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 one ? A DC 1 "O3'" A ? ? 1_555 A GMS 2 P A ? A DC 1 A GMS 2 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale2 covale one ? A DC 1 "O3'" B ? ? 1_555 A GMS 2 P B ? A DC 1 A GMS 2 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale3 covale both ? A GMS 2 "O3'" ? ? ? 1_555 A DC 3 P ? ? A GMS 2 A DC 3 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale4 covale one ? B DC 1 "O3'" ? ? ? 1_555 B GMS 2 P ? ? B DC 107 B GMS 108 1_555 ? ? ? ? ? ? ? 1.586 ? ? covale5 covale both ? B GMS 2 "O3'" ? ? ? 1_555 B DC 3 P ? ? B GMS 108 B DC 109 1_555 ? ? ? ? ? ? ? 1.637 ? ? metalc1 metalc ? ? B DG 6 N7 ? ? ? 1_555 D MG . MG ? ? B DG 112 B MG 301 1_555 ? ? ? ? ? ? ? 2.291 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 418 1_555 ? ? ? ? ? ? ? 2.206 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 420 1_555 ? ? ? ? ? ? ? 2.020 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 431 1_555 ? ? ? ? ? ? ? 2.031 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 437 1_555 ? ? ? ? ? ? ? 2.017 ? ? metalc6 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 301 B HOH 439 1_555 ? ? ? ? ? ? ? 1.989 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A GMS 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A GMS 2 B DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A GMS 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A GMS 2 B DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A GMS 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A GMS 2 B DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B GMS 2 N1 ? ? A DC 5 B GMS 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B GMS 2 O6 ? ? A DC 5 B GMS 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B GMS 2 N2 ? ? A DC 5 B GMS 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 107 1_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 N7 ? B DG 6 ? B DG 112 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 418 ? 1_555 89.2 ? 2 N7 ? B DG 6 ? B DG 112 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 420 ? 1_555 90.0 ? 3 O ? F HOH . ? B HOH 418 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 420 ? 1_555 96.0 ? 4 N7 ? B DG 6 ? B DG 112 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 431 ? 1_555 85.5 ? 5 O ? F HOH . ? B HOH 418 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 431 ? 1_555 174.6 ? 6 O ? F HOH . ? B HOH 420 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 431 ? 1_555 83.3 ? 7 N7 ? B DG 6 ? B DG 112 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 437 ? 1_555 178.8 ? 8 O ? F HOH . ? B HOH 418 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 437 ? 1_555 92.0 ? 9 O ? F HOH . ? B HOH 420 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 437 ? 1_555 89.8 ? 10 O ? F HOH . ? B HOH 431 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 437 ? 1_555 93.3 ? 11 N7 ? B DG 6 ? B DG 112 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 439 ? 1_555 92.3 ? 12 O ? F HOH . ? B HOH 418 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 439 ? 1_555 88.6 ? 13 O ? F HOH . ? B HOH 420 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 439 ? 1_555 174.9 ? 14 O ? F HOH . ? B HOH 431 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 439 ? 1_555 92.3 ? 15 O ? F HOH . ? B HOH 437 ? 1_555 MG ? D MG . ? B MG 301 ? 1_555 O ? F HOH . ? B HOH 439 ? 1_555 87.9 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SPM 201 ? 14 'BINDING SITE FOR RESIDUE SPM A 201' AC2 Software B MG 301 ? 6 'BINDING SITE FOR RESIDUE MG B 301' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 14 GMS A 2 ? GMS A 2 . ? 1_555 ? 2 AC1 14 DC A 3 ? DC A 3 . ? 1_455 ? 3 AC1 14 DG A 6 ? DG A 6 . ? 2_565 ? 4 AC1 14 HOH E . ? HOH A 401 . ? 1_455 ? 5 AC1 14 HOH E . ? HOH A 408 . ? 1_455 ? 6 AC1 14 HOH E . ? HOH A 438 . ? 1_455 ? 7 AC1 14 HOH E . ? HOH A 458 . ? 1_555 ? 8 AC1 14 GMS B 2 ? GMS B 108 . ? 2_465 ? 9 AC1 14 DG B 4 ? DG B 110 . ? 1_555 ? 10 AC1 14 DG B 4 ? DG B 110 . ? 3_546 ? 11 AC1 14 DC B 5 ? DC B 111 . ? 3_546 ? 12 AC1 14 DG B 6 ? DG B 112 . ? 3_546 ? 13 AC1 14 HOH F . ? HOH B 414 . ? 1_455 ? 14 AC1 14 HOH F . ? HOH B 444 . ? 2_465 ? 15 AC2 6 DG B 6 ? DG B 112 . ? 1_555 ? 16 AC2 6 HOH F . ? HOH B 418 . ? 1_555 ? 17 AC2 6 HOH F . ? HOH B 420 . ? 1_555 ? 18 AC2 6 HOH F . ? HOH B 431 . ? 1_555 ? 19 AC2 6 HOH F . ? HOH B 437 . ? 1_555 ? 20 AC2 6 HOH F . ? HOH B 439 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O B HOH 425 ? ? O B HOH 468 ? ? 2.08 2 1 O A HOH 459 ? ? O A HOH 463 ? ? 2.16 # 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 DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.43 108.30 2.13 0.30 N 2 1 C5 A DC 1 ? ? C6 A DC 1 ? ? N1 A DC 1 ? ? 124.23 121.00 3.23 0.50 N 3 1 "C3'" A DC 1 ? ? "O3'" A DC 1 ? B P A GMS 2 ? B 128.47 119.70 8.77 1.20 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 GMS 2 A GMS 2 ? DG ? 2 B GMS 2 B GMS 108 ? DG ? # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 GMS P P N R 72 GMS OP1 O N N 73 GMS SE SE N N 74 GMS "O5'" O N N 75 GMS N9 N Y N 76 GMS C4 C Y N 77 GMS N3 N N N 78 GMS C2 C N N 79 GMS N2 N N N 80 GMS N1 N N N 81 GMS C6 C N N 82 GMS O6 O N N 83 GMS C5 C Y N 84 GMS N7 N Y N 85 GMS C8 C Y N 86 GMS "C2'" C N N 87 GMS "C5'" C N N 88 GMS "C4'" C N R 89 GMS "O4'" O N N 90 GMS "C1'" C N R 91 GMS "C3'" C N S 92 GMS "O3'" O N N 93 GMS OP2 O N N 94 GMS HS H N N 95 GMS H21 H N N 96 GMS H22 H N N 97 GMS H1 H N N 98 GMS H8 H N N 99 GMS "H2'" H N N 100 GMS "H2''" H N N 101 GMS "H5'" H N N 102 GMS "H5''" H N N 103 GMS "H4'" H N N 104 GMS "H1'" H N N 105 GMS "H3'" H N N 106 GMS "HO3'" H N N 107 GMS HOP2 H N N 108 HOH O O N N 109 HOH H1 H N N 110 HOH H2 H N N 111 MG MG MG N N 112 SPM N1 N N N 113 SPM C2 C N N 114 SPM C3 C N N 115 SPM C4 C N N 116 SPM N5 N N N 117 SPM C6 C N N 118 SPM C7 C N N 119 SPM C8 C N N 120 SPM C9 C N N 121 SPM N10 N N N 122 SPM C11 C N N 123 SPM C12 C N N 124 SPM C13 C N N 125 SPM N14 N N N 126 SPM HN11 H N N 127 SPM HN12 H N N 128 SPM H21 H N N 129 SPM H22 H N N 130 SPM H31 H N N 131 SPM H32 H N N 132 SPM H41 H N N 133 SPM H42 H N N 134 SPM HN5 H N N 135 SPM H61 H N N 136 SPM H62 H N N 137 SPM H71 H N N 138 SPM H72 H N N 139 SPM H81 H N N 140 SPM H82 H N N 141 SPM H91 H N N 142 SPM H92 H N N 143 SPM HN0 H N N 144 SPM H111 H N N 145 SPM H112 H N N 146 SPM H121 H N N 147 SPM H122 H N N 148 SPM H131 H N N 149 SPM H132 H N N 150 SPM HN41 H N N 151 SPM HN42 H N N 152 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 GMS P OP1 doub N N 75 GMS P SE sing N N 76 GMS P "O5'" sing N N 77 GMS P OP2 sing N N 78 GMS SE HS sing N N 79 GMS "O5'" "C5'" sing N N 80 GMS N9 C4 sing Y N 81 GMS N9 C8 sing Y N 82 GMS N9 "C1'" sing N N 83 GMS C4 N3 sing N N 84 GMS C4 C5 doub Y N 85 GMS N3 C2 doub N N 86 GMS C2 N2 sing N N 87 GMS C2 N1 sing N N 88 GMS N2 H21 sing N N 89 GMS N2 H22 sing N N 90 GMS N1 C6 sing N N 91 GMS N1 H1 sing N N 92 GMS C6 O6 doub N N 93 GMS C6 C5 sing N N 94 GMS C5 N7 sing Y N 95 GMS N7 C8 doub Y N 96 GMS C8 H8 sing N N 97 GMS "C2'" "C1'" sing N N 98 GMS "C2'" "C3'" sing N N 99 GMS "C2'" "H2'" sing N N 100 GMS "C2'" "H2''" sing N N 101 GMS "C5'" "C4'" sing N N 102 GMS "C5'" "H5'" sing N N 103 GMS "C5'" "H5''" sing N N 104 GMS "C4'" "O4'" sing N N 105 GMS "C4'" "C3'" sing N N 106 GMS "C4'" "H4'" sing N N 107 GMS "O4'" "C1'" sing N N 108 GMS "C1'" "H1'" sing N N 109 GMS "C3'" "O3'" sing N N 110 GMS "C3'" "H3'" sing N N 111 GMS "O3'" "HO3'" sing N N 112 GMS OP2 HOP2 sing N N 113 HOH O H1 sing N N 114 HOH O H2 sing N N 115 SPM N1 C2 sing N N 116 SPM N1 HN11 sing N N 117 SPM N1 HN12 sing N N 118 SPM C2 C3 sing N N 119 SPM C2 H21 sing N N 120 SPM C2 H22 sing N N 121 SPM C3 C4 sing N N 122 SPM C3 H31 sing N N 123 SPM C3 H32 sing N N 124 SPM C4 N5 sing N N 125 SPM C4 H41 sing N N 126 SPM C4 H42 sing N N 127 SPM N5 C6 sing N N 128 SPM N5 HN5 sing N N 129 SPM C6 C7 sing N N 130 SPM C6 H61 sing N N 131 SPM C6 H62 sing N N 132 SPM C7 C8 sing N N 133 SPM C7 H71 sing N N 134 SPM C7 H72 sing N N 135 SPM C8 C9 sing N N 136 SPM C8 H81 sing N N 137 SPM C8 H82 sing N N 138 SPM C9 N10 sing N N 139 SPM C9 H91 sing N N 140 SPM C9 H92 sing N N 141 SPM N10 C11 sing N N 142 SPM N10 HN0 sing N N 143 SPM C11 C12 sing N N 144 SPM C11 H111 sing N N 145 SPM C11 H112 sing N N 146 SPM C12 C13 sing N N 147 SPM C12 H121 sing N N 148 SPM C12 H122 sing N N 149 SPM C13 N14 sing N N 150 SPM C13 H131 sing N N 151 SPM C13 H132 sing N N 152 SPM N14 HN41 sing N N 153 SPM N14 HN42 sing N N 154 # _ndb_struct_conf_na.entry_id 1VRO _ndb_struct_conf_na.feature 'z-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 DC 1 1_555 B DG 6 1_555 -0.346 -0.169 0.195 -5.715 4.355 2.504 1 A_DC1:DG112_B A 1 ? B 112 ? 19 1 1 A GMS 2 1_555 B DC 5 1_555 0.154 -0.116 0.003 -1.466 0.316 2.413 2 A_GMS2:DC111_B A 2 ? B 111 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 -0.190 -0.154 0.090 7.137 0.355 2.724 3 A_DC3:DG110_B A 3 ? B 110 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.252 -0.138 -0.016 -4.848 -3.457 1.198 4 A_DG4:DC109_B A 4 ? B 109 ? 19 1 1 A DC 5 1_555 B GMS 2 1_555 -0.269 -0.153 -0.063 7.284 -4.011 1.520 5 A_DC5:GMS108_B A 5 ? B 108 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.243 -0.141 0.039 -4.017 0.655 0.434 6 A_DG6:DC107_B A 6 ? B 107 ? 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 DC 1 1_555 B DG 6 1_555 A GMS 2 1_555 B DC 5 1_555 -0.052 5.145 3.371 -1.605 -1.020 -7.401 -34.895 -6.234 3.940 7.736 -12.170 -7.641 1 AA_DC1GMS2:DC111DG112_BB A 1 ? B 112 ? A 2 ? B 111 ? 1 A GMS 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 0.204 -0.895 3.231 -1.003 -2.512 -53.672 1.144 0.165 3.193 2.781 -1.110 -53.735 2 AA_GMS2DC3:DG110DC111_BB A 2 ? B 111 ? A 3 ? B 110 ? 1 A DC 3 1_555 B DG 4 1_555 A DG 4 1_555 B DC 3 1_555 0.009 5.458 3.769 0.339 -3.330 -5.811 -24.521 2.326 5.975 29.805 3.032 -6.705 3 AA_DC3DG4:DC109DG110_BB A 3 ? B 110 ? A 4 ? B 109 ? 1 A DG 4 1_555 B DC 3 1_555 A DC 5 1_555 B GMS 2 1_555 0.075 -1.054 3.216 -0.106 -5.671 -51.765 1.567 0.078 3.093 6.473 -0.121 -52.053 4 AA_DG4DC5:GMS108DC109_BB A 4 ? B 109 ? A 5 ? B 108 ? 1 A DC 5 1_555 B GMS 2 1_555 A DG 6 1_555 B DC 1 1_555 0.040 5.365 3.684 -0.482 -3.911 -6.079 -20.012 -2.450 5.989 32.727 -4.035 -7.244 5 AA_DC5DG6:DC107GMS108_BB A 5 ? B 108 ? A 6 ? B 107 ? # _atom_sites.entry_id 1VRO _atom_sites.fract_transf_matrix[1][1] 0.056249 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.031900 _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] 0.022668 _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 MG N O P SE # loop_