data_4RBO # _entry.id 4RBO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _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 4RBO pdb_00004rbo 10.2210/pdb4rbo/pdb NDB NA3168 ? ? RCSB RCSB087145 ? ? WWPDB D_1000087145 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-423217 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4RBO _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-09-12 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Joint Center for Structural Genomics (JCSG)' 1 'Partnership for Stem Cell Biology (STEMCELL)' 2 # _citation.id primary _citation.title ;Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells. ; _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 112 _citation.page_first 4666 _citation.page_last 4671 _citation.year 2015 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25825768 _citation.pdbx_database_id_DOI 10.1073/pnas.1502855112 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hayashi, Y.' 1 ? primary 'Caboni, L.' 2 ? primary 'Das, D.' 3 ? primary 'Yumoto, F.' 4 ? primary 'Clayton, T.' 5 ? primary 'Deller, M.C.' 6 ? primary 'Nguyen, P.' 7 ? primary 'Farr, C.L.' 8 ? primary 'Chiu, H.J.' 9 ? primary 'Miller, M.D.' 10 ? primary 'Elsliger, M.A.' 11 ? primary 'Deacon, A.M.' 12 ? primary 'Godzik, A.' 13 ? primary 'Lesley, S.A.' 14 ? primary 'Tomoda, K.' 15 ? primary 'Conklin, B.R.' 16 ? primary 'Wilson, I.A.' 17 ? primary 'Yamanaka, S.' 18 ? primary 'Fletterick, R.J.' 19 ? # _cell.entry_id 4RBO _cell.length_a 215.603 _cell.length_b 215.603 _cell.length_c 42.269 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 24 _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 4RBO _symmetry.Int_Tables_number 179 _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _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 man 'Putative homeobox protein NANOGP8' 8610.933 2 ? ? 'UNP residues 94-162' ? 2 polymer syn "5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3'" 3647.393 2 ? ? ? ? 3 polymer syn "5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3'" 3678.403 2 ? ? ? ? # 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 'polypeptide(L)' no no GKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKNNWPKNS GKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKNNWPKNS A,D JCSG-423217 2 polydeoxyribonucleotide no no '(DG)(DG)(DC)(DC)(DC)(DA)(DT)(DT)(DC)(DA)(DA)(DG)' GGCCCATTCAAG B,E ? 3 polydeoxyribonucleotide no no '(DC)(DT)(DT)(DG)(DA)(DA)(DT)(DG)(DG)(DG)(DC)(DC)' CTTGAATGGGCC C,F ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 LYS n 1 3 LYS n 1 4 GLN n 1 5 LYS n 1 6 THR n 1 7 ARG n 1 8 THR n 1 9 VAL n 1 10 PHE n 1 11 SER n 1 12 SER n 1 13 THR n 1 14 GLN n 1 15 LEU n 1 16 CYS n 1 17 VAL n 1 18 LEU n 1 19 ASN n 1 20 ASP n 1 21 ARG n 1 22 PHE n 1 23 GLN n 1 24 ARG n 1 25 GLN n 1 26 LYS n 1 27 TYR n 1 28 LEU n 1 29 SER n 1 30 LEU n 1 31 GLN n 1 32 GLN n 1 33 MET n 1 34 GLN n 1 35 GLU n 1 36 LEU n 1 37 SER n 1 38 ASN n 1 39 ILE n 1 40 LEU n 1 41 ASN n 1 42 LEU n 1 43 SER n 1 44 TYR n 1 45 LYS n 1 46 GLN n 1 47 VAL n 1 48 LYS n 1 49 THR n 1 50 TRP n 1 51 PHE n 1 52 GLN n 1 53 ASN n 1 54 GLN n 1 55 ARG n 1 56 MET n 1 57 LYS n 1 58 SER n 1 59 LYS n 1 60 ARG n 1 61 TRP n 1 62 GLN n 1 63 LYS n 1 64 ASN n 1 65 ASN n 1 66 TRP n 1 67 PRO n 1 68 LYS n 1 69 ASN n 1 70 SER n 2 1 DG n 2 2 DG n 2 3 DC n 2 4 DC n 2 5 DC n 2 6 DA n 2 7 DT n 2 8 DT n 2 9 DC n 2 10 DA n 2 11 DA n 2 12 DG n 3 1 DC n 3 2 DT n 3 3 DT n 3 4 DG n 3 5 DA n 3 6 DA n 3 7 DT n 3 8 DG n 3 9 DG n 3 10 DG n 3 11 DC n 3 12 DC n # _entity_src_gen.entity_id 1 _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 ? _entity_src_gen.pdbx_gene_src_gene 'NANOGP8, NM_024865' _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' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)Star' _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 46EkTevLIC _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # 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 NANP8_HUMAN Q6NSW7 1 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKNNWPKNS 94 ? 2 PDB 4RBO 4RBO 2 ? ? ? 3 PDB 4RBO 4RBO 3 ? ? ? # 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 4RBO A 2 ? 70 ? Q6NSW7 94 ? 162 ? 94 162 2 1 4RBO D 2 ? 70 ? Q6NSW7 94 ? 162 ? 94 162 3 2 4RBO B 1 ? 12 ? 4RBO 1 ? 12 ? 1 12 4 2 4RBO E 1 ? 12 ? 4RBO 1 ? 12 ? 1 12 5 3 4RBO C 1 ? 12 ? 4RBO 1 ? 12 ? 1 12 6 3 4RBO F 1 ? 12 ? 4RBO 1 ? 12 ? 1 12 # 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 4RBO GLY A 1 ? UNP Q6NSW7 ? ? 'expression tag' 0 1 2 4RBO GLY D 1 ? UNP Q6NSW7 ? ? 'expression tag' 0 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 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 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 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 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 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 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 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 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 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.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 4RBO # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 4.45 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 72.35 _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.pH 5.66 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details ;0.200M calcium acetate, 12.00% 2-propanol, 0.1M sodium cacodylate pH 5.66, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K ; _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.details 'Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)' _diffrn_detector.pdbx_collection_date 2013-02-22 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'single crystal Si(111) bent' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength 1.0 _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 4RBO _reflns.d_resolution_high 3.30 _reflns.d_resolution_low 29.899 _reflns.number_all 8834 _reflns.number_obs 8834 _reflns.pdbx_netI_over_sigmaI 9.400 _reflns.pdbx_Rsym_value 0.083 _reflns.pdbx_redundancy 3.400 _reflns.percent_possible_obs 97.000 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.pdbx_Rmerge_I_obs ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.meanI_over_sigI_obs 3.300 3.390 ? 1939 ? 0.552 0.552 ? 3.200 ? 602 94.300 1 1 ? 3.390 3.480 ? 2275 ? 0.426 0.426 ? 3.600 ? 639 97.200 2 1 ? 3.480 3.580 ? 2196 ? 0.489 0.489 ? 3.600 ? 613 98.600 3 1 ? 3.580 3.690 ? 2161 ? 0.353 0.353 ? 3.700 ? 582 99.100 4 1 ? 3.690 3.810 ? 2119 ? 0.268 0.268 ? 3.800 ? 565 96.000 5 1 ? 3.810 3.940 ? 1907 ? 0.275 0.275 ? 3.600 ? 537 96.100 6 1 ? 3.940 4.090 ? 1656 ? 0.222 0.222 ? 3.300 ? 496 93.200 7 1 ? 4.090 4.260 ? 1761 ? 0.137 0.137 ? 3.200 ? 542 98.700 8 1 ? 4.260 4.450 ? 1836 ? 0.142 0.142 ? 3.600 ? 504 100.000 9 1 ? 4.450 4.670 ? 1771 ? 0.112 0.112 ? 3.500 ? 505 99.600 10 1 ? 4.670 4.920 ? 1540 ? 0.108 0.108 ? 3.300 ? 467 99.700 11 1 ? 4.920 5.220 ? 1565 ? 0.077 0.077 ? 3.500 ? 444 97.000 12 1 ? 5.220 5.580 ? 1206 ? 0.063 0.063 ? 3.300 ? 371 91.500 13 1 ? 5.580 6.030 ? 1416 ? 0.069 0.069 ? 3.500 ? 409 99.300 14 1 ? 6.030 6.600 ? 1288 ? 0.072 0.072 ? 3.600 ? 361 99.400 15 1 ? 6.600 7.380 ? 1177 ? 0.055 0.055 ? 3.500 ? 335 97.500 16 1 ? 7.380 8.520 ? 819 ? 0.041 0.041 ? 2.900 ? 283 91.100 17 1 ? 8.520 10.440 ? 820 ? 0.040 0.040 ? 3.100 ? 262 99.100 18 1 ? 10.440 14.760 ? 649 ? 0.037 0.037 ? 3.100 ? 210 98.700 19 1 ? 14.760 29.899 ? 301 ? 0.020 0.020 ? 2.800 ? 107 82.200 20 1 ? # _refine.entry_id 4RBO _refine.ls_d_res_high 3.3000 _refine.ls_d_res_low 29.899 _refine.pdbx_ls_sigma_F 1.340 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 96.0700 _refine.ls_number_reflns_obs 8823 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2365 _refine.ls_R_factor_R_work 0.2349 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2682 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.7300 _refine.ls_number_reflns_R_free 417 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 188.3153 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.4800 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 325.040 _refine.B_iso_min 76.410 _refine.pdbx_overall_phase_error 30.1500 _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 932 _refine_hist.pdbx_number_atoms_nucleic_acid 972 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1904 _refine_hist.d_res_high 3.3000 _refine_hist.d_res_low 29.899 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 2036 0.003 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 2938 0.778 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 325 0.036 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 207 0.002 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 830 23.088 ? ? ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 3.3003 3.7771 3 96.0000 2703 . 0.2804 0.3111 . 153 . 2856 . . 'X-RAY DIFFRACTION' 3.7771 4.7556 3 96.0000 2763 . 0.2676 0.2935 . 137 . 2900 . . 'X-RAY DIFFRACTION' 4.7556 29.9000 3 96.0000 2940 . 0.2079 0.2393 . 127 . 3067 . . 'X-RAY DIFFRACTION' # _struct.entry_id 4RBO _struct.title 'Crystal structure of a Nanog homeobox (NANOG) from Homo sapiens at 3.30 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;Homeobox, PF00046 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Partnership for Stem Cell Biology, STEMCELL, Protein Structure Initiative, PSI-BIOLOGY, DNA BINDING PROTEIN, TRANSCRIPTION, TRANSCRIPTION-DNA complex ; _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN, TRANSCRIPTION/DNA' _struct_keywords.entry_id 4RBO # 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 1 ? E N N 2 ? F N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # 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 SER A 11 ? GLN A 25 ? SER A 103 GLN A 117 1 ? 15 HELX_P HELX_P2 2 SER A 29 ? LEU A 40 ? SER A 121 LEU A 132 1 ? 12 HELX_P HELX_P3 3 SER A 43 ? TRP A 61 ? SER A 135 TRP A 153 1 ? 19 HELX_P HELX_P4 4 SER D 11 ? GLN D 25 ? SER D 103 GLN D 117 1 ? 15 HELX_P HELX_P5 5 SER D 29 ? LEU D 40 ? SER D 121 LEU D 132 1 ? 12 HELX_P HELX_P6 6 SER D 43 ? TRP D 61 ? SER D 135 TRP D 153 1 ? 19 # _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 _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 16 SG ? ? ? 1_555 D CYS 16 SG ? ? A CYS 108 D CYS 108 1_556 ? ? ? ? ? ? ? 2.028 ? ? hydrog1 hydrog ? ? B DG 1 N1 ? ? ? 1_555 C DC 12 N3 ? ? B DG 1 C DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? B DG 1 N2 ? ? ? 1_555 C DC 12 O2 ? ? B DG 1 C DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? B DG 1 O6 ? ? ? 1_555 C DC 12 N4 ? ? B DG 1 C DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? B DG 2 N1 ? ? ? 1_555 C DC 11 N3 ? ? B DG 2 C DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? B DG 2 N2 ? ? ? 1_555 C DC 11 O2 ? ? B DG 2 C DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? B DG 2 O6 ? ? ? 1_555 C DC 11 N4 ? ? B DG 2 C DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? B DC 3 N3 ? ? ? 1_555 C DG 10 N1 ? ? B DC 3 C DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? B DC 3 N4 ? ? ? 1_555 C DG 10 O6 ? ? B DC 3 C DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? B DC 3 O2 ? ? ? 1_555 C DG 10 N2 ? ? B DC 3 C DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? B DC 4 N4 ? ? ? 1_555 C DG 8 O6 ? ? B DC 4 C DG 8 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog11 hydrog ? ? B DC 4 N3 ? ? ? 1_555 C DG 9 N1 ? ? B DC 4 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? B DC 4 N4 ? ? ? 1_555 C DG 9 O6 ? ? B DC 4 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B DC 4 O2 ? ? ? 1_555 C DG 9 N2 ? ? B DC 4 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? B DC 5 N4 ? ? ? 1_555 C DT 7 O4 ? ? B DC 5 C DT 7 1_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog15 hydrog ? ? B DC 5 N3 ? ? ? 1_555 C DG 8 N1 ? ? B DC 5 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? B DC 5 N4 ? ? ? 1_555 C DG 8 O6 ? ? B DC 5 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? B DC 5 O2 ? ? ? 1_555 C DG 8 N2 ? ? B DC 5 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? B DA 6 N1 ? ? ? 1_555 C DT 7 N3 ? ? B DA 6 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? B DA 6 N6 ? ? ? 1_555 C DT 7 O4 ? ? B DA 6 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B DT 7 N3 ? ? ? 1_555 C DA 6 N1 ? ? B DT 7 C DA 6 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog21 hydrog ? ? B DT 8 N3 ? ? ? 1_555 C DA 5 N1 ? ? B DT 8 C DA 5 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog22 hydrog ? ? B DC 9 N4 ? ? ? 1_555 C DT 3 O4 ? ? B DC 9 C DT 3 1_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog23 hydrog ? ? B DC 9 O2 ? ? ? 1_555 C DG 4 N2 ? ? B DC 9 C DG 4 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog24 hydrog ? ? B DA 10 N1 ? ? ? 1_555 C DT 3 N3 ? ? B DA 10 C DT 3 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog25 hydrog ? ? B DA 11 N1 ? ? ? 1_555 C DT 2 N3 ? ? B DA 11 C DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B DA 11 N6 ? ? ? 1_555 C DT 2 O4 ? ? B DA 11 C DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B DG 12 N1 ? ? ? 1_555 C DC 1 N3 ? ? B DG 12 C DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B DG 12 N2 ? ? ? 1_555 C DC 1 O2 ? ? B DG 12 C DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B DG 12 O6 ? ? ? 1_555 C DC 1 N4 ? ? B DG 12 C DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? E DG 1 O6 ? ? ? 1_555 F DC 11 N4 ? ? E DG 1 F DC 11 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog31 hydrog ? ? E DG 1 N2 ? ? ? 1_555 F DC 12 O2 ? ? E DG 1 F DC 12 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog32 hydrog ? ? E DG 2 O6 ? ? ? 1_555 F DG 10 N1 ? ? E DG 2 F DG 10 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog33 hydrog ? ? E DG 2 N1 ? ? ? 1_555 F DC 11 N3 ? ? E DG 2 F DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? E DG 2 N2 ? ? ? 1_555 F DC 11 O2 ? ? E DG 2 F DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? E DG 2 O6 ? ? ? 1_555 F DC 11 N4 ? ? E DG 2 F DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? E DC 3 N4 ? ? ? 1_555 F DG 9 O6 ? ? E DC 3 F DG 9 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog37 hydrog ? ? E DC 3 N3 ? ? ? 1_555 F DG 10 N1 ? ? E DC 3 F DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? E DC 3 N4 ? ? ? 1_555 F DG 10 O6 ? ? E DC 3 F DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? E DC 3 O2 ? ? ? 1_555 F DG 10 N2 ? ? E DC 3 F DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? E DC 4 N4 ? ? ? 1_555 F DG 8 O6 ? ? E DC 4 F DG 8 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog41 hydrog ? ? E DC 4 N3 ? ? ? 1_555 F DG 9 N1 ? ? E DC 4 F DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? E DC 4 N4 ? ? ? 1_555 F DG 9 O6 ? ? E DC 4 F DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? E DC 4 O2 ? ? ? 1_555 F DG 9 N2 ? ? E DC 4 F DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? E DC 5 N4 ? ? ? 1_555 F DT 7 O4 ? ? E DC 5 F DT 7 1_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog45 hydrog ? ? E DC 5 N3 ? ? ? 1_555 F DG 8 N1 ? ? E DC 5 F DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? E DC 5 N4 ? ? ? 1_555 F DG 8 O6 ? ? E DC 5 F DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? E DC 5 O2 ? ? ? 1_555 F DG 8 N2 ? ? E DC 5 F DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? E DA 6 N1 ? ? ? 1_555 F DT 7 N3 ? ? E DA 6 F DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? E DA 6 N6 ? ? ? 1_555 F DT 7 O4 ? ? E DA 6 F DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? E DT 7 N3 ? ? ? 1_555 F DA 6 N1 ? ? E DT 7 F DA 6 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog51 hydrog ? ? E DT 8 N3 ? ? ? 1_555 F DA 5 N1 ? ? E DT 8 F DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? E DT 8 O4 ? ? ? 1_555 F DA 5 N6 ? ? E DT 8 F DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? E DC 9 O2 ? ? ? 1_555 F DG 4 N2 ? ? E DC 9 F DG 4 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog54 hydrog ? ? E DA 10 N1 ? ? ? 1_555 F DT 3 N3 ? ? E DA 10 F DT 3 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog55 hydrog ? ? E DA 11 N1 ? ? ? 1_555 F DT 2 N3 ? ? E DA 11 F DT 2 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog56 hydrog ? ? E DG 12 N2 ? ? ? 1_555 F DC 1 O2 ? ? E DG 12 F DC 1 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? hydrog ? ? # _atom_sites.entry_id 4RBO _atom_sites.fract_transf_matrix[1][1] 0.004638 _atom_sites.fract_transf_matrix[1][2] 0.002678 _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] 0.005356 _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] 0.023658 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C H N O P S # 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 GLY 1 0 ? ? ? A . n A 1 2 LYS 2 94 ? ? ? A . n A 1 3 LYS 3 95 ? ? ? A . n A 1 4 GLN 4 96 ? ? ? A . n A 1 5 LYS 5 97 ? ? ? A . n A 1 6 THR 6 98 ? ? ? A . n A 1 7 ARG 7 99 ? ? ? A . n A 1 8 THR 8 100 100 THR THR A . n A 1 9 VAL 9 101 101 VAL VAL A . n A 1 10 PHE 10 102 102 PHE PHE A . n A 1 11 SER 11 103 103 SER SER A . n A 1 12 SER 12 104 104 SER SER A . n A 1 13 THR 13 105 105 THR THR A . n A 1 14 GLN 14 106 106 GLN GLN A . n A 1 15 LEU 15 107 107 LEU LEU A . n A 1 16 CYS 16 108 108 CYS CYS A . n A 1 17 VAL 17 109 109 VAL VAL A . n A 1 18 LEU 18 110 110 LEU LEU A . n A 1 19 ASN 19 111 111 ASN ASN A . n A 1 20 ASP 20 112 112 ASP ASP A . n A 1 21 ARG 21 113 113 ARG ARG A . n A 1 22 PHE 22 114 114 PHE PHE A . n A 1 23 GLN 23 115 115 GLN GLN A . n A 1 24 ARG 24 116 116 ARG ARG A . n A 1 25 GLN 25 117 117 GLN GLN A . n A 1 26 LYS 26 118 118 LYS LYS A . n A 1 27 TYR 27 119 119 TYR TYR A . n A 1 28 LEU 28 120 120 LEU LEU A . n A 1 29 SER 29 121 121 SER SER A . n A 1 30 LEU 30 122 122 LEU LEU A . n A 1 31 GLN 31 123 123 GLN GLN A . n A 1 32 GLN 32 124 124 GLN GLN A . n A 1 33 MET 33 125 125 MET MET A . n A 1 34 GLN 34 126 126 GLN GLN A . n A 1 35 GLU 35 127 127 GLU GLU A . n A 1 36 LEU 36 128 128 LEU LEU A . n A 1 37 SER 37 129 129 SER SER A . n A 1 38 ASN 38 130 130 ASN ASN A . n A 1 39 ILE 39 131 131 ILE ILE A . n A 1 40 LEU 40 132 132 LEU LEU A . n A 1 41 ASN 41 133 133 ASN ASN A . n A 1 42 LEU 42 134 134 LEU LEU A . n A 1 43 SER 43 135 135 SER SER A . n A 1 44 TYR 44 136 136 TYR TYR A . n A 1 45 LYS 45 137 137 LYS LYS A . n A 1 46 GLN 46 138 138 GLN GLN A . n A 1 47 VAL 47 139 139 VAL VAL A . n A 1 48 LYS 48 140 140 LYS LYS A . n A 1 49 THR 49 141 141 THR THR A . n A 1 50 TRP 50 142 142 TRP TRP A . n A 1 51 PHE 51 143 143 PHE PHE A . n A 1 52 GLN 52 144 144 GLN GLN A . n A 1 53 ASN 53 145 145 ASN ASN A . n A 1 54 GLN 54 146 146 GLN GLN A . n A 1 55 ARG 55 147 147 ARG ARG A . n A 1 56 MET 56 148 148 MET MET A . n A 1 57 LYS 57 149 149 LYS LYS A . n A 1 58 SER 58 150 150 SER SER A . n A 1 59 LYS 59 151 151 LYS LYS A . n A 1 60 ARG 60 152 152 ARG ARG A . n A 1 61 TRP 61 153 153 TRP TRP A . n A 1 62 GLN 62 154 154 GLN GLN A . n A 1 63 LYS 63 155 ? ? ? A . n A 1 64 ASN 64 156 ? ? ? A . n A 1 65 ASN 65 157 ? ? ? A . n A 1 66 TRP 66 158 ? ? ? A . n A 1 67 PRO 67 159 ? ? ? A . n A 1 68 LYS 68 160 ? ? ? A . n A 1 69 ASN 69 161 ? ? ? A . n A 1 70 SER 70 162 ? ? ? A . n B 2 1 DG 1 1 1 DG DG B . n B 2 2 DG 2 2 2 DG DG B . n B 2 3 DC 3 3 3 DC DC B . n B 2 4 DC 4 4 4 DC DC B . n B 2 5 DC 5 5 5 DC DC B . n B 2 6 DA 6 6 6 DA DA B . n B 2 7 DT 7 7 7 DT DT B . n B 2 8 DT 8 8 8 DT DT B . n B 2 9 DC 9 9 9 DC DC B . n B 2 10 DA 10 10 10 DA DA B . n B 2 11 DA 11 11 11 DA DA B . n B 2 12 DG 12 12 12 DG DG B . n C 3 1 DC 1 1 1 DC DC C . n C 3 2 DT 2 2 2 DT DT C . n C 3 3 DT 3 3 3 DT DT C . n C 3 4 DG 4 4 4 DG DG C . n C 3 5 DA 5 5 5 DA DA C . n C 3 6 DA 6 6 6 DA DA C . n C 3 7 DT 7 7 7 DT DT C . n C 3 8 DG 8 8 8 DG DG C . n C 3 9 DG 9 9 9 DG DG C . n C 3 10 DG 10 10 10 DG DG C . n C 3 11 DC 11 11 11 DC DC C . n C 3 12 DC 12 12 12 DC DC C . n D 1 1 GLY 1 0 ? ? ? D . n D 1 2 LYS 2 94 ? ? ? D . n D 1 3 LYS 3 95 ? ? ? D . n D 1 4 GLN 4 96 ? ? ? D . n D 1 5 LYS 5 97 ? ? ? D . n D 1 6 THR 6 98 ? ? ? D . n D 1 7 ARG 7 99 ? ? ? D . n D 1 8 THR 8 100 100 THR THR D . n D 1 9 VAL 9 101 101 VAL VAL D . n D 1 10 PHE 10 102 102 PHE PHE D . n D 1 11 SER 11 103 103 SER SER D . n D 1 12 SER 12 104 104 SER SER D . n D 1 13 THR 13 105 105 THR THR D . n D 1 14 GLN 14 106 106 GLN GLN D . n D 1 15 LEU 15 107 107 LEU LEU D . n D 1 16 CYS 16 108 108 CYS CYS D . n D 1 17 VAL 17 109 109 VAL VAL D . n D 1 18 LEU 18 110 110 LEU LEU D . n D 1 19 ASN 19 111 111 ASN ASN D . n D 1 20 ASP 20 112 112 ASP ASP D . n D 1 21 ARG 21 113 113 ARG ARG D . n D 1 22 PHE 22 114 114 PHE PHE D . n D 1 23 GLN 23 115 115 GLN GLN D . n D 1 24 ARG 24 116 116 ARG ARG D . n D 1 25 GLN 25 117 117 GLN GLN D . n D 1 26 LYS 26 118 118 LYS LYS D . n D 1 27 TYR 27 119 119 TYR TYR D . n D 1 28 LEU 28 120 120 LEU LEU D . n D 1 29 SER 29 121 121 SER SER D . n D 1 30 LEU 30 122 122 LEU LEU D . n D 1 31 GLN 31 123 123 GLN GLN D . n D 1 32 GLN 32 124 124 GLN GLN D . n D 1 33 MET 33 125 125 MET MET D . n D 1 34 GLN 34 126 126 GLN GLN D . n D 1 35 GLU 35 127 127 GLU GLU D . n D 1 36 LEU 36 128 128 LEU LEU D . n D 1 37 SER 37 129 129 SER SER D . n D 1 38 ASN 38 130 130 ASN ASN D . n D 1 39 ILE 39 131 131 ILE ILE D . n D 1 40 LEU 40 132 132 LEU LEU D . n D 1 41 ASN 41 133 133 ASN ASN D . n D 1 42 LEU 42 134 134 LEU LEU D . n D 1 43 SER 43 135 135 SER SER D . n D 1 44 TYR 44 136 136 TYR TYR D . n D 1 45 LYS 45 137 137 LYS LYS D . n D 1 46 GLN 46 138 138 GLN GLN D . n D 1 47 VAL 47 139 139 VAL VAL D . n D 1 48 LYS 48 140 140 LYS LYS D . n D 1 49 THR 49 141 141 THR THR D . n D 1 50 TRP 50 142 142 TRP TRP D . n D 1 51 PHE 51 143 143 PHE PHE D . n D 1 52 GLN 52 144 144 GLN GLN D . n D 1 53 ASN 53 145 145 ASN ASN D . n D 1 54 GLN 54 146 146 GLN GLN D . n D 1 55 ARG 55 147 147 ARG ARG D . n D 1 56 MET 56 148 148 MET MET D . n D 1 57 LYS 57 149 149 LYS LYS D . n D 1 58 SER 58 150 150 SER SER D . n D 1 59 LYS 59 151 151 LYS LYS D . n D 1 60 ARG 60 152 152 ARG ARG D . n D 1 61 TRP 61 153 153 TRP TRP D . n D 1 62 GLN 62 154 ? ? ? D . n D 1 63 LYS 63 155 ? ? ? D . n D 1 64 ASN 64 156 ? ? ? D . n D 1 65 ASN 65 157 ? ? ? D . n D 1 66 TRP 66 158 ? ? ? D . n D 1 67 PRO 67 159 ? ? ? D . n D 1 68 LYS 68 160 ? ? ? D . n D 1 69 ASN 69 161 ? ? ? D . n D 1 70 SER 70 162 ? ? ? D . n E 2 1 DG 1 1 1 DG DG E . n E 2 2 DG 2 2 2 DG DG E . n E 2 3 DC 3 3 3 DC DC E . n E 2 4 DC 4 4 4 DC DC E . n E 2 5 DC 5 5 5 DC DC E . n E 2 6 DA 6 6 6 DA DA E . n E 2 7 DT 7 7 7 DT DT E . n E 2 8 DT 8 8 8 DT DT E . n E 2 9 DC 9 9 9 DC DC E . n E 2 10 DA 10 10 10 DA DA E . n E 2 11 DA 11 11 11 DA DA E . n E 2 12 DG 12 12 12 DG DG E . n F 3 1 DC 1 1 1 DC DC F . n F 3 2 DT 2 2 2 DT DT F . n F 3 3 DT 3 3 3 DT DT F . n F 3 4 DG 4 4 4 DG DG F . n F 3 5 DA 5 5 5 DA DA F . n F 3 6 DA 6 6 6 DA DA F . n F 3 7 DT 7 7 7 DT DT F . n F 3 8 DG 8 8 8 DG DG F . n F 3 9 DG 9 9 9 DG DG F . n F 3 10 DG 10 10 10 DG DG F . n F 3 11 DC 11 11 11 DC DC F . n F 3 12 DC 12 12 12 DC DC F . n # loop_ _pdbx_SG_project.project_name _pdbx_SG_project.full_name_of_center _pdbx_SG_project.id _pdbx_SG_project.initial_of_center PSI:Biology 'Joint Center for Structural Genomics' 1 JCSG PSI:Biology 'Partnership for Stem Cell Biology' 2 STEMCELL # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA trimeric 3 2 author_and_software_defined_assembly PISA trimeric 3 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C 2 1 D,E,F # 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)' 2370 ? 1 MORE -21 ? 1 'SSA (A^2)' 7730 ? 2 'ABSA (A^2)' 2290 ? 2 MORE -19 ? 2 'SSA (A^2)' 7560 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_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 2014-10-01 2 'Structure model' 1 1 2015-04-08 3 'Structure model' 1 2 2015-04-29 4 'Structure model' 1 3 2017-11-22 5 'Structure model' 1 4 2023-02-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' database_2 3 5 'Structure model' struct_ref_seq_dif # 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 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' 5 5 'Structure model' '_struct_ref_seq_dif.details' # loop_ _pdbx_refine_tls.pdbx_refine_id _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[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 121.2803 110.5140 46.7518 0.9485 1.2723 1.0420 0.1095 -0.2282 0.0135 0.3914 0.6299 3.4839 0.7958 -1.6096 -1.3960 -0.3275 0.2215 -0.0082 0.3694 0.4547 0.1144 -0.6281 1.5177 -0.5774 'X-RAY DIFFRACTION' 2 ? refined 124.8855 123.2258 40.6024 0.7894 0.9774 1.1227 -0.1378 -0.2192 0.1046 1.4647 0.2148 3.4663 0.9129 -2.4538 -1.5656 -0.5546 0.3736 -0.0005 0.6171 0.5751 0.4921 -0.1187 -1.0788 0.2675 'X-RAY DIFFRACTION' 3 ? refined 124.6114 123.1968 39.0230 1.4261 0.7221 1.4195 -0.1448 -0.4113 0.0385 1.9168 0.0404 4.0348 1.1172 -2.9601 -1.8493 0.0137 0.5776 0.2563 -1.5123 0.5008 0.4078 -0.8117 -1.4029 0.2991 'X-RAY DIFFRACTION' 4 ? refined 122.0444 99.8007 25.7571 2.0677 1.6145 0.9790 -0.1177 0.0319 0.0603 2.5578 3.0781 0.5826 0.6460 1.4700 1.6177 -1.5164 1.0540 -0.0011 0.1908 0.2798 -0.4985 -0.7582 1.4063 -0.3094 'X-RAY DIFFRACTION' 5 ? refined 123.0005 85.8029 31.0926 1.6453 1.3955 1.7822 0.2892 0.0975 -0.0475 1.2662 1.3320 0.3969 -1.4690 1.2116 -0.8824 -1.2382 0.4635 0.0001 -0.3223 -1.6123 0.9773 0.5553 1.6906 0.8096 'X-RAY DIFFRACTION' 6 ? refined 123.2159 86.0311 32.8668 2.7525 1.9018 2.0894 -0.1215 0.4876 0.2474 0.3115 0.0014 -0.0503 -0.5227 0.2961 -0.1807 -0.4334 0.5401 -0.0012 -1.0354 -1.8512 -0.8408 0.1070 0.9698 0.8207 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 0 A 0 ;chain 'A' and (resid 100 through 154) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 2 2 B 0 B 0 ;chain 'B' and (resid 1 through 12) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 3 3 C 0 C 0 ;chain 'C' and (resid 1 through 12) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 4 4 D 0 D 0 ;chain 'D' and (resid 100 through 153) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 5 5 E 0 E 0 ;chain 'E' and (resid 1 through 12) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 6 6 F 0 F 0 ;chain 'F' and (resid 1 through 12) ; ? ? ? ? ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 PHASER 2.3.0 ? program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 4 SCALA 3.3.20 ? package 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' ? ? ? 5 PHENIX '(phenix.refine:' ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 6 MOSFLM . ? ? ? ? 'data reduction' ? ? ? # _pdbx_entry_details.entry_id 4RBO _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MAHHHHHHVDDDDKMSENLYFQ. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 94-162 OF THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 SG A CYS 108 ? ? 1_555 HG D CYS 108 ? ? 1_556 1.10 2 1 HG A CYS 108 ? ? 1_555 HG D CYS 108 ? ? 1_556 1.16 3 1 HG A CYS 108 ? ? 1_555 SG D CYS 108 ? ? 1_556 1.17 # 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'" C DA 6 ? ? "C1'" C DA 6 ? ? N9 C DA 6 ? ? 110.16 108.30 1.86 0.30 N 2 1 "O4'" C DG 9 ? ? "C1'" C DG 9 ? ? N9 C DG 9 ? ? 110.60 108.30 2.30 0.30 N 3 1 "O4'" C DG 10 ? ? "C1'" C DG 10 ? ? N9 C DG 10 ? ? 110.66 108.30 2.36 0.30 N 4 1 "O4'" E DC 3 ? ? "C1'" E DC 3 ? ? N1 E DC 3 ? ? 110.25 108.30 1.95 0.30 N 5 1 "O4'" E DC 4 ? ? "C1'" E DC 4 ? ? N1 E DC 4 ? ? 110.71 108.30 2.41 0.30 N 6 1 "O4'" F DA 6 ? ? "C1'" F DA 6 ? ? N9 F DA 6 ? ? 110.22 108.30 1.92 0.30 N # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id TRP _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 153 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -58.86 _pdbx_validate_torsion.psi 99.56 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 D LYS 140 ? CG ? D LYS 48 CG 2 1 Y 1 D LYS 140 ? CD ? D LYS 48 CD 3 1 Y 1 D LYS 140 ? CE ? D LYS 48 CE 4 1 Y 1 D LYS 140 ? NZ ? D LYS 48 NZ 5 1 Y 1 D TRP 153 ? CG ? D TRP 61 CG 6 1 Y 1 D TRP 153 ? CD1 ? D TRP 61 CD1 7 1 Y 1 D TRP 153 ? CD2 ? D TRP 61 CD2 8 1 Y 1 D TRP 153 ? NE1 ? D TRP 61 NE1 9 1 Y 1 D TRP 153 ? CE2 ? D TRP 61 CE2 10 1 Y 1 D TRP 153 ? CE3 ? D TRP 61 CE3 11 1 Y 1 D TRP 153 ? CZ2 ? D TRP 61 CZ2 12 1 Y 1 D TRP 153 ? CZ3 ? D TRP 61 CZ3 13 1 Y 1 D TRP 153 ? CH2 ? D TRP 61 CH2 # 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 GLY 0 ? A GLY 1 2 1 Y 1 A LYS 94 ? A LYS 2 3 1 Y 1 A LYS 95 ? A LYS 3 4 1 Y 1 A GLN 96 ? A GLN 4 5 1 Y 1 A LYS 97 ? A LYS 5 6 1 Y 1 A THR 98 ? A THR 6 7 1 Y 1 A ARG 99 ? A ARG 7 8 1 Y 1 A LYS 155 ? A LYS 63 9 1 Y 1 A ASN 156 ? A ASN 64 10 1 Y 1 A ASN 157 ? A ASN 65 11 1 Y 1 A TRP 158 ? A TRP 66 12 1 Y 1 A PRO 159 ? A PRO 67 13 1 Y 1 A LYS 160 ? A LYS 68 14 1 Y 1 A ASN 161 ? A ASN 69 15 1 Y 1 A SER 162 ? A SER 70 16 1 Y 1 D GLY 0 ? D GLY 1 17 1 Y 1 D LYS 94 ? D LYS 2 18 1 Y 1 D LYS 95 ? D LYS 3 19 1 Y 1 D GLN 96 ? D GLN 4 20 1 Y 1 D LYS 97 ? D LYS 5 21 1 Y 1 D THR 98 ? D THR 6 22 1 Y 1 D ARG 99 ? D ARG 7 23 1 Y 1 D GLN 154 ? D GLN 62 24 1 Y 1 D LYS 155 ? D LYS 63 25 1 Y 1 D ASN 156 ? D ASN 64 26 1 Y 1 D ASN 157 ? D ASN 65 27 1 Y 1 D TRP 158 ? D TRP 66 28 1 Y 1 D PRO 159 ? D PRO 67 29 1 Y 1 D LYS 160 ? D LYS 68 30 1 Y 1 D ASN 161 ? D ASN 69 31 1 Y 1 D SER 162 ? D SER 70 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4RBO 'double helix' 4RBO 'b-form double helix' 4RBO 'mismatched base pair' 4RBO 'triple 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 B DG 1 1_555 C DC 12 1_555 0.408 -0.224 0.542 0.247 -3.879 -2.693 1 B_DG1:DC12_C B 1 ? C 12 ? 19 1 1 B DG 2 1_555 C DC 11 1_555 -0.215 -0.200 0.107 9.022 -7.204 -1.078 2 B_DG2:DC11_C B 2 ? C 11 ? 19 1 1 B DC 3 1_555 C DG 10 1_555 0.023 -0.226 0.327 3.598 -13.976 -3.230 3 B_DC3:DG10_C B 3 ? C 10 ? 19 1 1 B DC 4 1_555 C DG 9 1_555 -0.366 -0.329 0.964 -11.258 -6.685 -5.178 4 B_DC4:DG9_C B 4 ? C 9 ? 19 1 1 B DC 5 1_555 C DG 8 1_555 -0.241 -0.466 1.262 -11.820 1.225 -3.219 5 B_DC5:DG8_C B 5 ? C 8 ? 19 1 1 B DA 6 1_555 C DT 7 1_555 0.208 -0.241 0.733 7.971 -19.347 3.329 6 B_DA6:DT7_C B 6 ? C 7 ? 20 1 1 B DT 7 1_555 C DA 6 1_555 0.188 0.051 0.544 3.966 -18.703 8.989 7 B_DT7:DA6_C B 7 ? C 6 ? ? 1 1 B DT 8 1_555 C DA 5 1_555 0.418 0.093 0.726 -2.070 -23.700 7.911 8 B_DT8:DA5_C B 8 ? C 5 ? ? 1 1 B DC 9 1_555 C DG 4 1_555 0.248 0.423 1.036 -9.407 -0.622 16.086 9 B_DC9:DG4_C B 9 ? C 4 ? ? 1 1 B DA 10 1_555 C DT 3 1_555 -0.214 0.152 0.911 4.709 -20.388 10.957 10 B_DA10:DT3_C B 10 ? C 3 ? ? 1 1 B DA 11 1_555 C DT 2 1_555 0.165 -0.210 0.572 5.896 -10.074 -7.908 11 B_DA11:DT2_C B 11 ? C 2 ? 20 1 1 B DG 12 1_555 C DC 1 1_555 -0.546 -0.032 0.228 7.126 -16.817 7.651 12 B_DG12:DC1_C B 12 ? C 1 ? 19 1 1 E DG 1 1_555 F DC 12 1_555 0.612 0.394 1.657 -5.237 -4.353 7.917 13 E_DG1:DC12_F E 1 ? F 12 ? ? ? 1 E DG 2 1_555 F DC 11 1_555 -0.121 -0.312 0.994 12.116 1.146 -2.525 14 E_DG2:DC11_F E 2 ? F 11 ? 19 1 1 E DC 3 1_555 F DG 10 1_555 -0.554 -0.146 1.184 2.295 -9.504 -0.301 15 E_DC3:DG10_F E 3 ? F 10 ? 19 1 1 E DC 4 1_555 F DG 8 1_555 -0.528 0.185 -1.640 -9.568 -3.417 -35.915 16 E_DC4:DG8_F E 4 ? F 8 ? ? ? 1 E DA 6 1_555 F DT 7 1_555 -0.289 -0.370 0.718 9.796 -19.796 4.888 17 E_DA6:DT7_F E 6 ? F 7 ? 20 1 1 E DT 7 1_555 F DA 6 1_555 0.384 0.320 0.487 3.537 -21.085 13.889 18 E_DT7:DA6_F E 7 ? F 6 ? ? 1 1 E DT 8 1_555 F DA 5 1_555 0.231 0.029 0.410 -0.326 -21.657 4.284 19 E_DT8:DA5_F E 8 ? F 5 ? 20 1 1 E DC 9 1_555 F DG 4 1_555 0.301 0.873 0.684 -7.464 2.038 22.574 20 E_DC9:DG4_F E 9 ? F 4 ? ? ? 1 E DA 10 1_555 F DT 3 1_555 -0.319 -0.057 0.445 3.048 -22.369 9.673 21 E_DA10:DT3_F E 10 ? F 3 ? ? 1 1 E DA 11 1_555 F DT 2 1_555 0.242 0.361 0.358 6.548 -17.551 7.441 22 E_DA11:DT2_F E 11 ? F 2 ? ? ? 1 E DG 12 1_555 F DC 1 1_555 0.818 0.979 0.780 8.821 -32.144 32.737 23 E_DG12:DC1_F E 12 ? F 1 ? ? 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 B DG 1 1_555 C DC 12 1_555 B DG 2 1_555 C DC 11 1_555 0.183 -0.394 3.220 7.228 10.442 31.555 -2.306 0.816 2.919 18.301 -12.668 33.955 1 BB_DG1DG2:DC11DC12_CC B 1 ? C 12 ? B 2 ? C 11 ? 1 B DG 2 1_555 C DC 11 1_555 B DC 3 1_555 C DG 10 1_555 -0.039 -0.740 3.257 -2.118 5.524 35.214 -1.990 -0.237 3.106 9.052 3.470 35.692 2 BB_DG2DC3:DG10DC11_CC B 2 ? C 11 ? B 3 ? C 10 ? 1 B DC 3 1_555 C DG 10 1_555 B DC 4 1_555 C DG 9 1_555 -0.133 -0.738 3.540 -4.304 5.678 35.167 -2.067 -0.442 3.376 9.281 7.035 35.859 3 BB_DC3DC4:DG9DG10_CC B 3 ? C 10 ? B 4 ? C 9 ? 1 B DC 4 1_555 C DG 9 1_555 B DC 5 1_555 C DG 8 1_555 0.277 -0.730 3.406 -2.739 3.763 33.290 -1.895 -0.938 3.274 6.528 4.751 33.605 4 BB_DC4DC5:DG8DG9_CC B 4 ? C 9 ? B 5 ? C 8 ? 1 B DC 5 1_555 C DG 8 1_555 B DA 6 1_555 C DT 7 1_555 0.097 0.196 2.896 4.170 -1.159 35.352 0.469 0.379 2.881 -1.899 -6.835 35.608 5 BB_DC5DA6:DT7DG8_CC B 5 ? C 8 ? B 6 ? C 7 ? 1 B DA 6 1_555 C DT 7 1_555 B DT 7 1_555 C DA 6 1_555 0.867 -0.977 3.380 1.076 -3.219 34.276 -1.123 -1.289 3.479 -5.445 -1.820 34.439 6 BB_DA6DT7:DA6DT7_CC B 6 ? C 7 ? B 7 ? C 6 ? 1 B DT 7 1_555 C DA 6 1_555 B DT 8 1_555 C DA 5 1_555 -0.303 -0.627 3.453 1.443 -2.090 35.364 -0.705 0.722 3.469 -3.434 -2.371 35.453 7 BB_DT7DT8:DA5DA6_CC B 7 ? C 6 ? B 8 ? C 5 ? 1 B DT 8 1_555 C DA 5 1_555 B DC 9 1_555 C DG 4 1_555 1.283 0.542 3.521 1.166 2.608 35.869 0.474 -1.897 3.589 4.226 -1.889 35.979 8 BB_DT8DC9:DG4DA5_CC B 8 ? C 5 ? B 9 ? C 4 ? 1 B DC 9 1_555 C DG 4 1_555 B DA 10 1_555 C DT 3 1_555 -1.154 0.904 2.973 -0.211 4.189 32.280 0.935 2.026 3.070 7.494 0.377 32.544 9 BB_DC9DA10:DT3DG4_CC B 9 ? C 4 ? B 10 ? C 3 ? 1 B DA 10 1_555 C DT 3 1_555 B DA 11 1_555 C DT 2 1_555 -0.880 -0.251 3.268 -1.544 0.870 34.261 -0.563 1.248 3.297 1.475 2.618 34.305 10 BB_DA10DA11:DT2DT3_CC B 10 ? C 3 ? B 11 ? C 2 ? 1 B DA 11 1_555 C DT 2 1_555 B DG 12 1_555 C DC 1 1_555 0.295 -0.654 3.268 -0.707 1.275 36.701 -1.211 -0.564 3.238 2.023 1.122 36.729 11 BB_DA11DG12:DC1DT2_CC B 11 ? C 2 ? B 12 ? C 1 ? 1 E DG 1 1_555 F DC 12 1_555 E DG 2 1_555 F DC 11 1_555 -0.560 -0.166 3.137 5.533 6.044 31.336 -1.301 1.924 2.916 10.957 -10.030 32.363 12 EE_DG1DG2:DC11DC12_FF E 1 ? F 12 ? E 2 ? F 11 ? 1 E DG 2 1_555 F DC 11 1_555 E DC 3 1_555 F DG 10 1_555 0.249 -0.934 3.504 -1.889 3.252 32.196 -2.277 -0.798 3.376 5.839 3.391 32.409 13 EE_DG2DC3:DG10DC11_FF E 2 ? F 11 ? E 3 ? F 10 ? 1 E DC 3 1_555 F DG 10 1_555 E DC 4 1_555 F DG 8 1_555 0.093 -0.958 5.195 -5.029 3.199 53.457 -1.374 -0.598 5.107 3.543 5.571 53.763 14 EE_DC3DC4:DG8DG10_FF E 3 ? F 10 ? E 4 ? F 8 ? 1 E DC 4 1_555 F DG 8 1_555 E DA 6 1_555 F DT 7 1_555 0.111 -0.206 4.788 8.578 1.732 51.549 -0.402 0.707 4.740 1.976 -9.782 52.237 15 EE_DC4DA6:DT7DG8_FF E 4 ? F 8 ? E 6 ? F 7 ? 1 E DA 6 1_555 F DT 7 1_555 E DT 7 1_555 F DA 6 1_555 1.048 -0.614 3.409 1.982 -1.486 37.360 -0.752 -1.359 3.479 -2.317 -3.089 37.439 16 EE_DA6DT7:DA6DT7_FF E 6 ? F 7 ? E 7 ? F 6 ? 1 E DT 7 1_555 F DA 6 1_555 E DT 8 1_555 F DA 5 1_555 -0.792 -0.786 3.224 0.195 -1.246 33.628 -1.156 1.399 3.246 -2.153 -0.338 33.651 17 EE_DT7DT8:DA5DA6_FF E 7 ? F 6 ? E 8 ? F 5 ? 1 E DT 8 1_555 F DA 5 1_555 E DC 9 1_555 F DG 4 1_555 1.753 0.619 3.411 2.389 5.167 36.103 0.223 -2.442 3.567 8.273 -3.826 36.534 18 EE_DT8DC9:DG4DA5_FF E 8 ? F 5 ? E 9 ? F 4 ? 1 E DC 9 1_555 F DG 4 1_555 E DA 10 1_555 F DT 3 1_555 -1.700 1.027 3.106 0.219 6.476 31.161 0.713 3.142 3.237 11.894 -0.402 31.811 19 EE_DC9DA10:DT3DG4_FF E 9 ? F 4 ? E 10 ? F 3 ? 1 E DA 10 1_555 F DT 3 1_555 E DA 11 1_555 F DT 2 1_555 0.165 0.047 3.203 -0.609 0.527 35.160 0.001 -0.362 3.200 0.872 1.008 35.169 20 EE_DA10DA11:DT2DT3_FF E 10 ? F 3 ? E 11 ? F 2 ? 1 E DA 11 1_555 F DT 2 1_555 E DG 12 1_555 F DC 1 1_555 0.377 -0.282 3.213 -1.860 5.090 39.098 -1.003 -0.772 3.133 7.561 2.763 39.457 21 EE_DA11DG12:DC1DT2_FF E 11 ? F 2 ? E 12 ? F 1 ? #