data_2P2R # _entry.id 2P2R # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.313 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2P2R NDB PD0977 RCSB RCSB041892 WWPDB D_1000041892 # _pdbx_database_status.entry_id 2P2R _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-03-07 _pdbx_database_status.status_code REL _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'James, T.L.' 1 'Stroud, R.M.' 2 'Du, Z.' 3 'Fenn, S.' 4 'Tjhen, R.' 5 'Lee, J.K.' 6 # _citation.id primary _citation.title ;Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 35 _citation.page_first 2651 _citation.page_last 2660 _citation.year 2007 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17426136 _citation.pdbx_database_id_DOI 10.1093/nar/gkm139 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Fenn, S.' 1 ? primary 'Du, Z.' 2 ? primary 'Lee, J.K.' 3 ? primary 'Tjhen, R.' 4 ? primary 'Stroud, R.M.' 5 ? primary 'James, T.L.' 6 ? # _cell.entry_id 2P2R _cell.length_a 81.069 _cell.length_b 81.069 _cell.length_c 87.815 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _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 2P2R _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'C-rich strand of human telomeric DNA' 2066.401 1 ? ? 'third KH domain of human Poly(C)-binding Protein 2' ? 2 polymer man 'Poly(rC)-binding protein 2' 8135.047 1 ? ? ? ? 3 non-polymer syn '6-AMINOPYRIMIDIN-2(1H)-ONE' 111.102 1 ? ? ? ? 4 water nat water 18.015 81 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Alpha-CP2, hnRNP-E2' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DA)(DA)(DC)(DC)(DC)(DT)(DA)' AACCCTA B ? 2 'polypeptide(L)' no yes 'KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQ(MSE)SGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSET' KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSET A ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DA n 1 3 DC n 1 4 DC n 1 5 DC n 1 6 DT n 1 7 DA n 2 1 LYS n 2 2 ALA n 2 3 GLN n 2 4 THR n 2 5 THR n 2 6 SER n 2 7 HIS n 2 8 GLU n 2 9 LEU n 2 10 THR n 2 11 ILE n 2 12 PRO n 2 13 ASN n 2 14 ASP n 2 15 LEU n 2 16 ILE n 2 17 GLY n 2 18 CYS n 2 19 ILE n 2 20 ILE n 2 21 GLY n 2 22 ARG n 2 23 GLN n 2 24 GLY n 2 25 ALA n 2 26 LYS n 2 27 ILE n 2 28 ASN n 2 29 GLU n 2 30 ILE n 2 31 ARG n 2 32 GLN n 2 33 MSE n 2 34 SER n 2 35 GLY n 2 36 ALA n 2 37 GLN n 2 38 ILE n 2 39 LYS n 2 40 ILE n 2 41 ALA n 2 42 ASN n 2 43 PRO n 2 44 VAL n 2 45 GLU n 2 46 GLY n 2 47 SER n 2 48 THR n 2 49 ASP n 2 50 ARG n 2 51 GLN n 2 52 VAL n 2 53 THR n 2 54 ILE n 2 55 THR n 2 56 GLY n 2 57 SER n 2 58 ALA n 2 59 ALA n 2 60 SER n 2 61 ILE n 2 62 SER n 2 63 LEU n 2 64 ALA n 2 65 GLN n 2 66 TYR n 2 67 LEU n 2 68 ILE n 2 69 ASN n 2 70 VAL n 2 71 ARG n 2 72 LEU n 2 73 SER n 2 74 SER n 2 75 GLU n 2 76 THR n # _entity_src_gen.entity_id 2 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene PCBP2 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'bl21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pet24a _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _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 'this sequence in present in human telomeric DNA' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP PCBP2_HUMAN Q15366 2 AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINVRLSSET 285 ? 2 PDB 2P2R 2P2R 1 AACCCTA ? ? # 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 2P2R A 2 ? 76 ? Q15366 285 ? 359 ? 285 359 2 2 2P2R B 1 ? 7 ? 2P2R 498 ? 504 ? 498 504 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2P2R LYS A 1 ? UNP Q15366 ? ? 'EXPRESSION TAG' 284 1 1 2P2R MSE A 33 ? UNP Q15366 MET 316 'MODIFIED RESIDUE' 316 2 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 CYT non-polymer . '6-AMINOPYRIMIDIN-2(1H)-ONE' CYTOSINE 'C4 H5 N3 O' 111.102 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2P2R _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.78 _exptl_crystal.density_percent_sol 55.71 _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 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.18 _exptl_crystal_grow.pdbx_details '2M ammonium sulfate, 80 mM lithium sulfate, 100 mM CAPS, pH 8.18, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K' _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.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 'ammonium sulfate' ? ? ? 1 2 1 'lithium sulfate' ? ? ? 1 3 1 CAPS ? ? ? 1 4 1 glycerol ? ? ? 1 5 1 water ? ? ? 1 6 2 'ammonium sulfate' ? ? ? 1 7 2 'lithium sulfate' ? ? ? 1 8 2 CAPS ? ? ? 1 9 2 glycerol ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2006-06-28 _diffrn_detector.details 'KOHZU: Double Crystal Si(111)' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'double crystal SI(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.11588 1.0 2 0.97945 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 8.3.1' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 8.3.1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '1.11588, 0.97945' # _reflns.entry_id 2P2R _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 54.80 _reflns.d_resolution_high 1.6 _reflns.number_obs 15516 _reflns.number_all 15752 _reflns.percent_possible_obs 98.5 _reflns.pdbx_Rmerge_I_obs .033 _reflns.pdbx_Rsym_value .036 _reflns.pdbx_netI_over_sigmaI 22.8 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.8 _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 1.6 _reflns_shell.d_res_low 1.642 _reflns_shell.percent_possible_all 84.66 _reflns_shell.Rmerge_I_obs 0.406 _reflns_shell.pdbx_Rsym_value .382 _reflns_shell.meanI_over_sigI_obs 7.3 _reflns_shell.pdbx_redundancy 3.6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _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 2P2R _refine.ls_number_reflns_obs 13842 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 54.80 _refine.ls_d_res_high 1.60 _refine.ls_percent_reflns_obs 98.04 _refine.ls_R_factor_obs 0.20660 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20482 _refine.ls_R_factor_R_free 0.24225 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 723 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.952 _refine.correlation_coeff_Fo_to_Fc_free 0.939 _refine.B_iso_mean 28.797 _refine.aniso_B[1][1] 0.49 _refine.aniso_B[2][2] 0.49 _refine.aniso_B[3][3] -0.73 _refine.aniso_B[1][2] 0.24 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _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 ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.104 _refine.pdbx_overall_ESU_R_Free 0.095 _refine.overall_SU_ML 0.056 _refine.overall_SU_B 3.052 _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 569 _refine_hist.pdbx_number_atoms_nucleic_acid 137 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 81 _refine_hist.number_atoms_total 795 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 54.80 # 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 0.010 0.022 ? 730 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.349 2.212 ? 1019 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 4.443 5.000 ? 80 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 35.648 25.652 ? 23 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 10.647 15.000 ? 106 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 23.314 15.000 ? 4 'X-RAY DIFFRACTION' ? r_chiral_restr 0.090 0.200 ? 124 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 496 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.205 0.200 ? 346 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.301 0.200 ? 508 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.124 0.200 ? 51 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.125 0.200 ? 32 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.178 0.200 ? 8 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 1.559 1.500 ? 387 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.225 2.000 ? 613 'X-RAY DIFFRACTION' ? r_scbond_it 2.710 3.000 ? 417 'X-RAY DIFFRACTION' ? r_scangle_it 3.661 4.500 ? 403 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.600 _refine_ls_shell.d_res_low 1.642 _refine_ls_shell.number_reflns_R_work 874 _refine_ls_shell.R_factor_R_work 0.285 _refine_ls_shell.percent_reflns_obs 84.68 _refine_ls_shell.R_factor_R_free 0.302 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 49 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2P2R _struct.title 'Crystal structure of the third KH domain of human Poly(C)-Binding Protein-2 in complex with C-rich strand of human telomeric DNA' _struct.pdbx_descriptor 'Poly(rC)-binding protein 2/DNA Complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2P2R _struct_keywords.pdbx_keywords 'RNA AND DNA BINDING PROTEIN/DNA' _struct_keywords.text 'PROTEIN-DNA COMPLEX, RNA AND DNA BINDING PROTEIN-DNA COMPLEX' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details 'The biological assembly is a monomer' # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASN B 13 ? GLY B 21 ? ASN A 296 GLY A 304 1 ? 9 HELX_P HELX_P2 2 GLY B 24 ? GLY B 35 ? GLY A 307 GLY A 318 1 ? 12 HELX_P HELX_P3 3 SER B 57 ? SER B 73 ? SER A 340 SER A 356 1 ? 17 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 covale1 covale both ? B GLN 32 C ? ? ? 1_555 B MSE 33 N ? ? A GLN 315 A MSE 316 1_555 ? ? ? ? ? ? ? 1.325 ? covale2 covale both ? B MSE 33 C ? ? ? 1_555 B SER 34 N ? ? A MSE 316 A SER 317 1_555 ? ? ? ? ? ? ? 1.335 ? hydrog1 hydrog ? ? A DA 2 N3 ? ? ? 1_555 A DC 3 N4 ? ? B DA 499 B DC 500 1_555 ? ? ? ? ? ? 'DA-DC MISPAIR' ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 3 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 THR B 5 ? PRO B 12 ? THR A 288 PRO A 295 A 2 ASP B 49 ? GLY B 56 ? ASP A 332 GLY A 339 A 3 GLN B 37 ? ILE B 40 ? GLN A 320 ILE A 323 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N LEU B 9 ? N LEU A 292 O VAL B 52 ? O VAL A 335 A 2 3 O THR B 55 ? O THR A 338 N GLN B 37 ? N GLN A 320 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _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 4 _struct_site.details 'BINDING SITE FOR RESIDUE CYT A 501' # 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 4 HOH E . ? HOH A 76 . ? 1_555 ? 2 AC1 4 MSE B 33 ? MSE A 316 . ? 3_665 ? 3 AC1 4 SER B 34 ? SER A 317 . ? 3_665 ? 4 AC1 4 ALA B 59 ? ALA A 342 . ? 3_665 ? # _atom_sites.entry_id 2P2R _atom_sites.fract_transf_matrix[1][1] 0.012335 _atom_sites.fract_transf_matrix[1][2] 0.007122 _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] 0.014243 _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] 0.011388 _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 S SE # 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 DA 1 498 498 DA A B . n A 1 2 DA 2 499 499 DA A B . n A 1 3 DC 3 500 500 DC C B . n A 1 4 DC 4 501 501 DC C B . n A 1 5 DC 5 502 502 DC C B . n A 1 6 DT 6 503 503 DT T B . n A 1 7 DA 7 504 504 DA A B . n B 2 1 LYS 1 284 ? ? ? A . n B 2 2 ALA 2 285 ? ? ? A . n B 2 3 GLN 3 286 286 GLN GLN A . n B 2 4 THR 4 287 287 THR THR A . n B 2 5 THR 5 288 288 THR THR A . n B 2 6 SER 6 289 289 SER SER A . n B 2 7 HIS 7 290 290 HIS HIS A . n B 2 8 GLU 8 291 291 GLU GLU A . n B 2 9 LEU 9 292 292 LEU LEU A . n B 2 10 THR 10 293 293 THR THR A . n B 2 11 ILE 11 294 294 ILE ILE A . n B 2 12 PRO 12 295 295 PRO PRO A . n B 2 13 ASN 13 296 296 ASN ASN A . n B 2 14 ASP 14 297 297 ASP ASP A . n B 2 15 LEU 15 298 298 LEU LEU A . n B 2 16 ILE 16 299 299 ILE ILE A . n B 2 17 GLY 17 300 300 GLY GLY A . n B 2 18 CYS 18 301 301 CYS CYS A . n B 2 19 ILE 19 302 302 ILE ILE A . n B 2 20 ILE 20 303 303 ILE ILE A . n B 2 21 GLY 21 304 304 GLY GLY A . n B 2 22 ARG 22 305 305 ARG ARG A . n B 2 23 GLN 23 306 306 GLN GLN A . n B 2 24 GLY 24 307 307 GLY GLY A . n B 2 25 ALA 25 308 308 ALA ALA A . n B 2 26 LYS 26 309 309 LYS LYS A . n B 2 27 ILE 27 310 310 ILE ILE A . n B 2 28 ASN 28 311 311 ASN ASN A . n B 2 29 GLU 29 312 312 GLU GLU A . n B 2 30 ILE 30 313 313 ILE ILE A . n B 2 31 ARG 31 314 314 ARG ARG A . n B 2 32 GLN 32 315 315 GLN GLN A . n B 2 33 MSE 33 316 316 MSE MSE A . n B 2 34 SER 34 317 317 SER SER A . n B 2 35 GLY 35 318 318 GLY GLY A . n B 2 36 ALA 36 319 319 ALA ALA A . n B 2 37 GLN 37 320 320 GLN GLN A . n B 2 38 ILE 38 321 321 ILE ILE A . n B 2 39 LYS 39 322 322 LYS LYS A . n B 2 40 ILE 40 323 323 ILE ILE A . n B 2 41 ALA 41 324 324 ALA ALA A . n B 2 42 ASN 42 325 325 ASN ASN A . n B 2 43 PRO 43 326 326 PRO PRO A . n B 2 44 VAL 44 327 327 VAL VAL A . n B 2 45 GLU 45 328 328 GLU GLU A . n B 2 46 GLY 46 329 329 GLY GLY A . n B 2 47 SER 47 330 330 SER SER A . n B 2 48 THR 48 331 331 THR THR A . n B 2 49 ASP 49 332 332 ASP ASP A . n B 2 50 ARG 50 333 333 ARG ARG A . n B 2 51 GLN 51 334 334 GLN GLN A . n B 2 52 VAL 52 335 335 VAL VAL A . n B 2 53 THR 53 336 336 THR THR A . n B 2 54 ILE 54 337 337 ILE ILE A . n B 2 55 THR 55 338 338 THR THR A . n B 2 56 GLY 56 339 339 GLY GLY A . n B 2 57 SER 57 340 340 SER SER A . n B 2 58 ALA 58 341 341 ALA ALA A . n B 2 59 ALA 59 342 342 ALA ALA A . n B 2 60 SER 60 343 343 SER SER A . n B 2 61 ILE 61 344 344 ILE ILE A . n B 2 62 SER 62 345 345 SER SER A . n B 2 63 LEU 63 346 346 LEU LEU A . n B 2 64 ALA 64 347 347 ALA ALA A . n B 2 65 GLN 65 348 348 GLN GLN A . n B 2 66 TYR 66 349 349 TYR TYR A . n B 2 67 LEU 67 350 350 LEU LEU A . n B 2 68 ILE 68 351 351 ILE ILE A . n B 2 69 ASN 69 352 352 ASN ASN A . n B 2 70 VAL 70 353 353 VAL VAL A . n B 2 71 ARG 71 354 354 ARG ARG A . n B 2 72 LEU 72 355 355 LEU LEU A . n B 2 73 SER 73 356 356 SER SER A . n B 2 74 SER 74 357 357 SER SER A . n B 2 75 GLU 75 358 358 GLU GLU A . n B 2 76 THR 76 359 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 CYT 1 501 501 CYT CYT A . D 4 HOH 1 12 12 HOH HOH B . D 4 HOH 2 13 13 HOH HOH B . D 4 HOH 3 15 15 HOH HOH B . D 4 HOH 4 22 22 HOH HOH B . D 4 HOH 5 25 25 HOH HOH B . D 4 HOH 6 31 31 HOH HOH B . D 4 HOH 7 33 33 HOH HOH B . D 4 HOH 8 35 35 HOH HOH B . D 4 HOH 9 40 40 HOH HOH B . D 4 HOH 10 47 47 HOH HOH B . D 4 HOH 11 59 59 HOH HOH B . D 4 HOH 12 60 60 HOH HOH B . D 4 HOH 13 67 67 HOH HOH B . D 4 HOH 14 68 68 HOH HOH B . D 4 HOH 15 70 70 HOH HOH B . D 4 HOH 16 72 72 HOH HOH B . D 4 HOH 17 73 73 HOH HOH B . D 4 HOH 18 78 78 HOH HOH B . D 4 HOH 19 82 82 HOH HOH B . E 4 HOH 1 1 1 HOH HOH A . E 4 HOH 2 2 2 HOH HOH A . E 4 HOH 3 3 3 HOH HOH A . E 4 HOH 4 4 4 HOH HOH A . E 4 HOH 5 5 5 HOH HOH A . E 4 HOH 6 6 6 HOH HOH A . E 4 HOH 7 7 7 HOH HOH A . E 4 HOH 8 8 8 HOH HOH A . E 4 HOH 9 9 9 HOH HOH A . E 4 HOH 10 10 10 HOH HOH A . E 4 HOH 11 11 11 HOH HOH A . E 4 HOH 12 14 14 HOH HOH A . E 4 HOH 13 16 16 HOH HOH A . E 4 HOH 14 17 17 HOH HOH A . E 4 HOH 15 18 18 HOH HOH A . E 4 HOH 16 19 19 HOH HOH A . E 4 HOH 17 20 20 HOH HOH A . E 4 HOH 18 21 21 HOH HOH A . E 4 HOH 19 23 23 HOH HOH A . E 4 HOH 20 24 24 HOH HOH A . E 4 HOH 21 26 26 HOH HOH A . E 4 HOH 22 27 27 HOH HOH A . E 4 HOH 23 28 28 HOH HOH A . E 4 HOH 24 29 29 HOH HOH A . E 4 HOH 25 30 30 HOH HOH A . E 4 HOH 26 32 32 HOH HOH A . E 4 HOH 27 34 34 HOH HOH A . E 4 HOH 28 36 36 HOH HOH A . E 4 HOH 29 37 37 HOH HOH A . E 4 HOH 30 38 38 HOH HOH A . E 4 HOH 31 39 39 HOH HOH A . E 4 HOH 32 42 42 HOH HOH A . E 4 HOH 33 43 43 HOH HOH A . E 4 HOH 34 44 44 HOH HOH A . E 4 HOH 35 45 45 HOH HOH A . E 4 HOH 36 46 46 HOH HOH A . E 4 HOH 37 48 48 HOH HOH A . E 4 HOH 38 49 49 HOH HOH A . E 4 HOH 39 50 50 HOH HOH A . E 4 HOH 40 51 51 HOH HOH A . E 4 HOH 41 52 52 HOH HOH A . E 4 HOH 42 53 53 HOH HOH A . E 4 HOH 43 54 54 HOH HOH A . E 4 HOH 44 55 55 HOH HOH A . E 4 HOH 45 56 56 HOH HOH A . E 4 HOH 46 57 57 HOH HOH A . E 4 HOH 47 58 58 HOH HOH A . E 4 HOH 48 61 61 HOH HOH A . E 4 HOH 49 62 62 HOH HOH A . E 4 HOH 50 63 63 HOH HOH A . E 4 HOH 51 64 64 HOH HOH A . E 4 HOH 52 65 65 HOH HOH A . E 4 HOH 53 66 66 HOH HOH A . E 4 HOH 54 69 69 HOH HOH A . E 4 HOH 55 71 71 HOH HOH A . E 4 HOH 56 74 74 HOH HOH A . E 4 HOH 57 75 75 HOH HOH A . E 4 HOH 58 76 76 HOH HOH A . E 4 HOH 59 77 77 HOH HOH A . E 4 HOH 60 79 79 HOH HOH A . E 4 HOH 61 80 80 HOH HOH A . E 4 HOH 62 81 81 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id B _pdbx_struct_mod_residue.label_comp_id MSE _pdbx_struct_mod_residue.label_seq_id 33 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MSE _pdbx_struct_mod_residue.auth_seq_id 316 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id MET _pdbx_struct_mod_residue.details SELENOMETHIONINE # _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 # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 9 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2007-06-12 2 'Structure model' 1 1 2007-10-16 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2019-07-24 # _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 ? # 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' Advisory 4 4 'Structure model' 'Refinement description' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Derived calculations' 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 4 'Structure model' pdbx_unobs_or_zero_occ_atoms 2 4 'Structure model' software 3 5 'Structure model' software 4 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_software.classification' 2 5 'Structure model' '_software.contact_author' 3 5 'Structure model' '_software.contact_author_email' 4 5 'Structure model' '_software.language' 5 5 'Structure model' '_software.location' 6 5 'Structure model' '_software.name' 7 5 'Structure model' '_software.type' 8 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.pdbx_refine_id 1 ? refined 28.6070 16.7040 42.7230 -0.0686 -0.0871 0.0320 -0.0035 -0.0017 -0.0120 3.4952 1.4278 0.4185 -0.9139 -0.3362 -0.0924 -0.0374 -0.0244 -0.1967 -0.0105 -0.0121 0.0432 -0.0364 0.0143 0.0494 'X-RAY DIFFRACTION' 2 ? refined 19.9330 14.9330 37.7130 -0.1941 -0.1594 0.0763 -0.0104 -0.0121 -0.0700 5.5050 10.4674 8.5610 -3.2472 2.2764 -3.6751 0.3055 0.3895 -0.5774 -0.1224 -0.1881 0.4838 0.0134 0.0910 -0.1174 '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 287 B 4 A 357 B 74 ? 'X-RAY DIFFRACTION' ? 2 2 B 498 A 1 B 504 A 7 ? 'X-RAY DIFFRACTION' ? # _pdbx_phasing_dm_shell.d_res_high 1.700 _pdbx_phasing_dm_shell.d_res_low 60.000 _pdbx_phasing_dm_shell.delta_phi_final 0.160 _pdbx_phasing_dm_shell.delta_phi_initial ? _pdbx_phasing_dm_shell.fom_acentric ? _pdbx_phasing_dm_shell.fom_centric ? _pdbx_phasing_dm_shell.fom 0.166 _pdbx_phasing_dm_shell.reflns_acentric ? _pdbx_phasing_dm_shell.reflns_centric ? _pdbx_phasing_dm_shell.reflns 22307 # _phasing.method SAD # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal REFMAC . ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu phasing http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 3 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 4 DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 5 PDB_EXTRACT 2.000 'April. 3, 2006' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 6 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 7 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? 8 # 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'" B DT 503 ? ? "C1'" B DT 503 ? ? N1 B DT 503 ? ? 110.48 108.30 2.18 0.30 N 2 1 "O4'" B DA 504 ? ? "C4'" B DA 504 ? ? "C3'" B DA 504 ? ? 101.77 104.50 -2.73 0.40 N 3 1 "O4'" B DA 504 ? ? "C1'" B DA 504 ? ? N9 B DA 504 ? ? 112.50 108.30 4.20 0.30 N # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A LYS 284 ? B LYS 1 2 1 Y 1 A ALA 285 ? B ALA 2 3 1 Y 1 A THR 359 ? B THR 76 # _ndb_struct_conf_na.entry_id 2P2R _ndb_struct_conf_na.feature 'double helix' # _ndb_struct_na_base_pair.model_number 1 _ndb_struct_na_base_pair.i_label_asym_id A _ndb_struct_na_base_pair.i_label_comp_id DA _ndb_struct_na_base_pair.i_label_seq_id 2 _ndb_struct_na_base_pair.i_symmetry 1_555 _ndb_struct_na_base_pair.j_label_asym_id A _ndb_struct_na_base_pair.j_label_comp_id DC _ndb_struct_na_base_pair.j_label_seq_id 3 _ndb_struct_na_base_pair.j_symmetry 1_555 _ndb_struct_na_base_pair.shear -7.679 _ndb_struct_na_base_pair.stretch 0.812 _ndb_struct_na_base_pair.stagger -0.539 _ndb_struct_na_base_pair.buckle 6.834 _ndb_struct_na_base_pair.propeller -3.200 _ndb_struct_na_base_pair.opening -9.530 _ndb_struct_na_base_pair.pair_number 1 _ndb_struct_na_base_pair.pair_name B_DA499:DC500_B _ndb_struct_na_base_pair.i_auth_asym_id B _ndb_struct_na_base_pair.i_auth_seq_id 499 _ndb_struct_na_base_pair.i_PDB_ins_code ? _ndb_struct_na_base_pair.j_auth_asym_id B _ndb_struct_na_base_pair.j_auth_seq_id 500 _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 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 '6-AMINOPYRIMIDIN-2(1H)-ONE' CYT 4 water HOH #