data_2XSE # _entry.id 2XSE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2XSE PDBE EBI-45557 WWPDB D_1290045557 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2XSE _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2010-09-28 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Heidebrecht, T.' 1 'Christodoulou, E.' 2 'Chalmers, M.J.' 3 'Jan, S.' 4 'ter Riete, B.' 5 'Grover, R.K.' 6 'Joosten, R.P.' 7 'Littler, D.' 8 'vanLuenen, H.' 9 'Griffin, P.R.' 10 'Wentworth, P.' 11 'Borst, P.' 12 'Perrakis, A.' 13 # _citation.id primary _citation.title 'The Structural Basis for Recognition of Base J Containing DNA by a Novel DNA Binding Domain in Jbp1.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 39 _citation.page_first 5715 _citation.page_last ? _citation.year 2011 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21415010 _citation.pdbx_database_id_DOI 10.1093/NAR/GKR125 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Heidebrecht, T.' 1 primary 'Christodoulou, E.' 2 primary 'Chalmers, M.J.' 3 primary 'Jan, S.' 4 primary 'Ter Riet, B.' 5 primary 'Grover, R.K.' 6 primary 'Joosten, R.P.' 7 primary 'Littler, D.' 8 primary 'Van Luenen, H.' 9 primary 'Griffin, P.R.' 10 primary 'Wentworth, P.' 11 primary 'Borst, P.' 12 primary 'Perrakis, A.' 13 # _cell.entry_id 2XSE _cell.length_a 67.338 _cell.length_b 67.338 _cell.length_c 186.762 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XSE _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 # 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 'THYMINE DIOXYGENASE JBP1' 20537.340 1 1.14.11.6 ? 'DNA-BINDING DOMAIN, RESIDUES 392-561' ? 2 non-polymer syn 'NITRATE ION' 62.005 1 ? ? ? ? 3 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 4 water nat water 18.015 164 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'J-BINDING PROTEIN 1' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;TNL(MSE)VSTAVEKKKYLDSEFLLHCISAQLLD(MSE)WKQARARWLELVGKEWAH(MSE)LALNPERKDFLWKNQSE (MSE)NSAFFDLCEVGKQV(MSE)LGLLGKEVALPKEEQAFWI(MSE)YAVHLSAACAEELH(MSE)PEVA(MSE)SLRK LNVKLKDFNFGGTRYFKD(MSE)PPEEKKRR(MSE)ERKQRIEEARRHG(MSE)P ; _entity_poly.pdbx_seq_one_letter_code_can ;TNLMVSTAVEKKKYLDSEFLLHCISAQLLDMWKQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFFDLCEVGK QVMLGLLGKEVALPKEEQAFWIMYAVHLSAACAEELHMPEVAMSLRKLNVKLKDFNFGGTRYFKDMPPEEKKRRMERKQR IEEARRHGMP ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 THR n 1 2 ASN n 1 3 LEU n 1 4 MSE n 1 5 VAL n 1 6 SER n 1 7 THR n 1 8 ALA n 1 9 VAL n 1 10 GLU n 1 11 LYS n 1 12 LYS n 1 13 LYS n 1 14 TYR n 1 15 LEU n 1 16 ASP n 1 17 SER n 1 18 GLU n 1 19 PHE n 1 20 LEU n 1 21 LEU n 1 22 HIS n 1 23 CYS n 1 24 ILE n 1 25 SER n 1 26 ALA n 1 27 GLN n 1 28 LEU n 1 29 LEU n 1 30 ASP n 1 31 MSE n 1 32 TRP n 1 33 LYS n 1 34 GLN n 1 35 ALA n 1 36 ARG n 1 37 ALA n 1 38 ARG n 1 39 TRP n 1 40 LEU n 1 41 GLU n 1 42 LEU n 1 43 VAL n 1 44 GLY n 1 45 LYS n 1 46 GLU n 1 47 TRP n 1 48 ALA n 1 49 HIS n 1 50 MSE n 1 51 LEU n 1 52 ALA n 1 53 LEU n 1 54 ASN n 1 55 PRO n 1 56 GLU n 1 57 ARG n 1 58 LYS n 1 59 ASP n 1 60 PHE n 1 61 LEU n 1 62 TRP n 1 63 LYS n 1 64 ASN n 1 65 GLN n 1 66 SER n 1 67 GLU n 1 68 MSE n 1 69 ASN n 1 70 SER n 1 71 ALA n 1 72 PHE n 1 73 PHE n 1 74 ASP n 1 75 LEU n 1 76 CYS n 1 77 GLU n 1 78 VAL n 1 79 GLY n 1 80 LYS n 1 81 GLN n 1 82 VAL n 1 83 MSE n 1 84 LEU n 1 85 GLY n 1 86 LEU n 1 87 LEU n 1 88 GLY n 1 89 LYS n 1 90 GLU n 1 91 VAL n 1 92 ALA n 1 93 LEU n 1 94 PRO n 1 95 LYS n 1 96 GLU n 1 97 GLU n 1 98 GLN n 1 99 ALA n 1 100 PHE n 1 101 TRP n 1 102 ILE n 1 103 MSE n 1 104 TYR n 1 105 ALA n 1 106 VAL n 1 107 HIS n 1 108 LEU n 1 109 SER n 1 110 ALA n 1 111 ALA n 1 112 CYS n 1 113 ALA n 1 114 GLU n 1 115 GLU n 1 116 LEU n 1 117 HIS n 1 118 MSE n 1 119 PRO n 1 120 GLU n 1 121 VAL n 1 122 ALA n 1 123 MSE n 1 124 SER n 1 125 LEU n 1 126 ARG n 1 127 LYS n 1 128 LEU n 1 129 ASN n 1 130 VAL n 1 131 LYS n 1 132 LEU n 1 133 LYS n 1 134 ASP n 1 135 PHE n 1 136 ASN n 1 137 PHE n 1 138 GLY n 1 139 GLY n 1 140 THR n 1 141 ARG n 1 142 TYR n 1 143 PHE n 1 144 LYS n 1 145 ASP n 1 146 MSE n 1 147 PRO n 1 148 PRO n 1 149 GLU n 1 150 GLU n 1 151 LYS n 1 152 LYS n 1 153 ARG n 1 154 ARG n 1 155 MSE n 1 156 GLU n 1 157 ARG n 1 158 LYS n 1 159 GLN n 1 160 ARG n 1 161 ILE n 1 162 GLU n 1 163 GLU n 1 164 ALA n 1 165 ARG n 1 166 ARG n 1 167 HIS n 1 168 GLY n 1 169 MSE n 1 170 PRO 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 ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _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 'LEISHMANIA TARENTOLAE' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 5689 _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 511693 _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 _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 ? _entity_src_gen.pdbx_host_org_vector LIC _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code JBP1_LEITA _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession Q9U6M1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2XSE _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 170 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9U6M1 _struct_ref_seq.db_align_beg 392 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 561 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 392 _struct_ref_seq.pdbx_auth_seq_align_end 561 # 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 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 NO3 non-polymer . 'NITRATE ION' ? 'N O3 -1' 62.005 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.entry_id 2XSE _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.83 _exptl_crystal.density_percent_sol 56 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '20MM HEPES PH 7.5, 50MM NACL, 1MM TCEP 15.3% PEG 6000, 0.2M POTASSIUM NITRATE, 20% GLYCEROL (CRYO-PROTECTANT)' # _diffrn.id 1 _diffrn.ambient_temp 77 _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.pdbx_collection_date 2010-03-20 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.978 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X06SA' _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X06SA _diffrn_source.pdbx_wavelength 0.978 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2XSE _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.00 _reflns.d_resolution_high 1.90 _reflns.number_obs 20683 _reflns.number_all ? _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.09 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 10.90 _reflns.B_iso_Wilson_estimate 36 _reflns.pdbx_redundancy 5.2 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.90 _reflns_shell.d_res_low 2.00 _reflns_shell.percent_possible_all 98.3 _reflns_shell.Rmerge_I_obs 0.66 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.30 _reflns_shell.pdbx_redundancy 5.4 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2XSE _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 19541 _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 58.32 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 99.58 _refine.ls_R_factor_obs 0.17553 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.17420 _refine.ls_R_factor_R_free 0.20038 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 1055 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.954 _refine.correlation_coeff_Fo_to_Fc_free 0.951 _refine.B_iso_mean 45.111 _refine.aniso_B[1][1] 0.66 _refine.aniso_B[2][2] 0.66 _refine.aniso_B[3][3] -0.99 _refine.aniso_B[1][2] 0.33 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. ; _refine.pdbx_starting_model NONE _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 0.115 _refine.pdbx_overall_ESU_R_Free 0.109 _refine.overall_SU_ML 0.073 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 4.741 _refine.overall_SU_R_Cruickshank_DPI ? _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 1320 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 10 _refine_hist.number_atoms_solvent 164 _refine_hist.number_atoms_total 1494 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 58.32 # 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 0.013 0.022 ? 1420 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 1031 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.255 1.970 ? 1913 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.888 3.000 ? 2511 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 4.386 5.000 ? 176 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 34.578 23.824 ? 68 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 13.070 15.000 ? 288 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 16.458 15.000 ? 11 'X-RAY DIFFRACTION' ? r_chiral_restr 0.082 0.200 ? 199 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 1556 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 290 'X-RAY DIFFRACTION' ? r_nbd_refined 0.258 0.200 ? 494 'X-RAY DIFFRACTION' ? r_nbd_other 0.170 0.200 ? 953 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.174 0.200 ? 649 'X-RAY DIFFRACTION' ? r_nbtor_other 0.085 0.200 ? 620 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.118 0.200 ? 21 '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 0.349 0.200 ? 19 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.195 0.200 ? 25 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.020 0.200 ? 2 '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 0.058 0.200 ? 1420 'X-RAY DIFFRACTION' ? r_mcbond_other 0.016 0.200 ? 1031 'X-RAY DIFFRACTION' ? r_mcangle_it 0.073 0.300 ? 1906 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? '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_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.899 _refine_ls_shell.d_res_low 1.948 _refine_ls_shell.number_reflns_R_work 1350 _refine_ls_shell.R_factor_R_work 0.235 _refine_ls_shell.percent_reflns_obs 97.02 _refine_ls_shell.R_factor_R_free 0.230 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 83 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2XSE _struct.title 'The structural basis for recognition of J-base containing DNA by a novel DNA-binding domain in JBP1' _struct.pdbx_descriptor 'THYMINE DIOXYGENASE JBP1 (E.C.1.14.11.6)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2XSE _struct_keywords.pdbx_keywords OXIDOREDUCTASE _struct_keywords.text 'OXIDOREDUCTASE, DNA-BINDING' # 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 ? # _struct_biol.id 1 # 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 MSE A 4 ? LYS A 11 ? MSE A 395 LYS A 402 1 ? 8 HELX_P HELX_P2 2 LYS A 12 ? LEU A 15 ? LYS A 403 LEU A 406 5 ? 4 HELX_P HELX_P3 3 ASP A 16 ? LEU A 21 ? ASP A 407 LEU A 412 1 ? 6 HELX_P HELX_P4 4 SER A 25 ? ASN A 54 ? SER A 416 ASN A 445 1 ? 30 HELX_P HELX_P5 5 SER A 66 ? GLY A 88 ? SER A 457 GLY A 479 1 ? 23 HELX_P HELX_P6 6 LEU A 93 ? GLU A 115 ? LEU A 484 GLU A 506 1 ? 23 HELX_P HELX_P7 7 SER A 124 ? PHE A 137 ? SER A 515 PHE A 528 1 ? 14 HELX_P HELX_P8 8 PRO A 147 ? ARG A 166 ? PRO A 538 ARG A 557 1 ? 20 # _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 ? ? A MSE 4 C ? ? ? 1_555 A VAL 5 N ? ? A MSE 395 A VAL 396 1_555 ? ? ? ? ? ? ? 1.334 ? covale2 covale ? ? A ASP 30 C ? ? ? 1_555 A MSE 31 N ? ? A ASP 421 A MSE 422 1_555 ? ? ? ? ? ? ? 1.333 ? covale3 covale ? ? A MSE 31 C ? ? ? 1_555 A TRP 32 N ? ? A MSE 422 A TRP 423 1_555 ? ? ? ? ? ? ? 1.333 ? covale4 covale ? ? A HIS 49 C ? ? ? 1_555 A MSE 50 N ? ? A HIS 440 A MSE 441 1_555 ? ? ? ? ? ? ? 1.325 ? covale5 covale ? ? A MSE 50 C ? ? ? 1_555 A LEU 51 N ? ? A MSE 441 A LEU 442 1_555 ? ? ? ? ? ? ? 1.318 ? covale6 covale ? ? A GLU 67 C ? ? ? 1_555 A MSE 68 N ? ? A GLU 458 A MSE 459 1_555 ? ? ? ? ? ? ? 1.331 ? covale7 covale ? ? A MSE 68 C ? ? ? 1_555 A ASN 69 N ? ? A MSE 459 A ASN 460 1_555 ? ? ? ? ? ? ? 1.327 ? covale8 covale ? ? A VAL 82 C ? ? ? 1_555 A MSE 83 N ? ? A VAL 473 A MSE 474 1_555 ? ? ? ? ? ? ? 1.326 ? covale9 covale ? ? A MSE 83 C ? ? ? 1_555 A LEU 84 N ? ? A MSE 474 A LEU 475 1_555 ? ? ? ? ? ? ? 1.326 ? covale10 covale ? ? A ILE 102 C ? ? ? 1_555 A MSE 103 N ? ? A ILE 493 A MSE 494 1_555 ? ? ? ? ? ? ? 1.340 ? covale11 covale ? ? A MSE 103 C ? ? ? 1_555 A TYR 104 N ? ? A MSE 494 A TYR 495 1_555 ? ? ? ? ? ? ? 1.330 ? covale12 covale ? ? A HIS 117 C ? ? ? 1_555 A MSE 118 N ? ? A HIS 508 A MSE 509 1_555 ? ? ? ? ? ? ? 1.323 ? covale13 covale ? ? A MSE 118 C ? ? ? 1_555 A PRO 119 N ? ? A MSE 509 A PRO 510 1_555 ? ? ? ? ? ? ? 1.349 ? covale14 covale ? ? A ALA 122 C ? ? ? 1_555 A MSE 123 N ? ? A ALA 513 A MSE 514 1_555 ? ? ? ? ? ? ? 1.340 ? covale15 covale ? ? A MSE 123 C ? ? ? 1_555 A SER 124 N ? ? A MSE 514 A SER 515 1_555 ? ? ? ? ? ? ? 1.324 ? covale16 covale ? ? A ASP 145 C ? ? ? 1_555 A MSE 146 N ? ? A ASP 536 A MSE 537 1_555 ? ? ? ? ? ? ? 1.330 ? covale17 covale ? ? A MSE 146 C ? ? ? 1_555 A PRO 147 N ? ? A MSE 537 A PRO 538 1_555 ? ? ? ? ? ? ? 1.350 ? covale18 covale ? ? A ARG 154 C ? ? ? 1_555 A MSE 155 N B ? A ARG 545 A MSE 546 1_555 ? ? ? ? ? ? ? 1.330 ? covale19 covale ? ? A ARG 154 C ? ? ? 1_555 A MSE 155 N A ? A ARG 545 A MSE 546 1_555 ? ? ? ? ? ? ? 1.330 ? covale20 covale ? ? A MSE 155 C B ? ? 1_555 A GLU 156 N ? ? A MSE 546 A GLU 547 1_555 ? ? ? ? ? ? ? 1.331 ? covale21 covale ? ? A MSE 155 C A ? ? 1_555 A GLU 156 N ? ? A MSE 546 A GLU 547 1_555 ? ? ? ? ? ? ? 1.330 ? covale22 covale ? ? A GLY 168 C ? ? ? 1_555 A MSE 169 N ? ? A GLY 559 A MSE 560 1_555 ? ? ? ? ? ? ? 1.339 ? covale23 covale ? ? A MSE 169 C ? ? ? 1_555 A PRO 170 N ? ? A MSE 560 A PRO 561 1_555 ? ? ? ? ? ? ? 1.351 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE NO3 A 1562' AC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE GOL A 1563' # 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 7 ASN A 54 ? ASN A 445 . ? 6_665 ? 2 AC1 7 GLU A 56 ? GLU A 447 . ? 6_665 ? 3 AC1 7 LEU A 93 ? LEU A 484 . ? 11_555 ? 4 AC1 7 PRO A 94 ? PRO A 485 . ? 11_555 ? 5 AC1 7 LYS A 95 ? LYS A 486 . ? 11_555 ? 6 AC1 7 LYS A 95 ? LYS A 486 . ? 1_555 ? 7 AC1 7 HOH D . ? HOH A 2161 . ? 1_555 ? 8 AC2 6 GLU A 90 ? GLU A 481 . ? 7_455 ? 9 AC2 6 SER A 124 ? SER A 515 . ? 1_555 ? 10 AC2 6 ARG A 126 ? ARG A 517 . ? 1_555 ? 11 AC2 6 LYS A 127 ? LYS A 518 . ? 1_555 ? 12 AC2 6 HOH D . ? HOH A 2057 . ? 1_555 ? 13 AC2 6 HOH D . ? HOH A 2162 . ? 1_555 ? # _database_PDB_matrix.entry_id 2XSE _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2XSE _atom_sites.fract_transf_matrix[1][1] 0.014850 _atom_sites.fract_transf_matrix[1][2] 0.008574 _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] 0.017148 _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] 0.005354 _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 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 THR 1 392 ? ? ? A . n A 1 2 ASN 2 393 ? ? ? A . n A 1 3 LEU 3 394 ? ? ? A . n A 1 4 MSE 4 395 395 MSE MSE A . n A 1 5 VAL 5 396 396 VAL VAL A . n A 1 6 SER 6 397 397 SER SER A . n A 1 7 THR 7 398 398 THR THR A . n A 1 8 ALA 8 399 399 ALA ALA A . n A 1 9 VAL 9 400 400 VAL VAL A . n A 1 10 GLU 10 401 401 GLU GLU A . n A 1 11 LYS 11 402 402 LYS LYS A . n A 1 12 LYS 12 403 403 LYS LYS A . n A 1 13 LYS 13 404 404 LYS LYS A . n A 1 14 TYR 14 405 405 TYR TYR A . n A 1 15 LEU 15 406 406 LEU LEU A . n A 1 16 ASP 16 407 407 ASP ASP A . n A 1 17 SER 17 408 408 SER SER A . n A 1 18 GLU 18 409 409 GLU GLU A . n A 1 19 PHE 19 410 410 PHE PHE A . n A 1 20 LEU 20 411 411 LEU LEU A . n A 1 21 LEU 21 412 412 LEU LEU A . n A 1 22 HIS 22 413 413 HIS HIS A . n A 1 23 CYS 23 414 414 CYS CYS A . n A 1 24 ILE 24 415 415 ILE ILE A . n A 1 25 SER 25 416 416 SER SER A . n A 1 26 ALA 26 417 417 ALA ALA A . n A 1 27 GLN 27 418 418 GLN GLN A . n A 1 28 LEU 28 419 419 LEU LEU A . n A 1 29 LEU 29 420 420 LEU LEU A . n A 1 30 ASP 30 421 421 ASP ASP A . n A 1 31 MSE 31 422 422 MSE MSE A . n A 1 32 TRP 32 423 423 TRP TRP A . n A 1 33 LYS 33 424 424 LYS LYS A . n A 1 34 GLN 34 425 425 GLN GLN A . n A 1 35 ALA 35 426 426 ALA ALA A . n A 1 36 ARG 36 427 427 ARG ARG A . n A 1 37 ALA 37 428 428 ALA ALA A . n A 1 38 ARG 38 429 429 ARG ARG A . n A 1 39 TRP 39 430 430 TRP TRP A . n A 1 40 LEU 40 431 431 LEU LEU A . n A 1 41 GLU 41 432 432 GLU GLU A . n A 1 42 LEU 42 433 433 LEU LEU A . n A 1 43 VAL 43 434 434 VAL VAL A . n A 1 44 GLY 44 435 435 GLY GLY A . n A 1 45 LYS 45 436 436 LYS LYS A . n A 1 46 GLU 46 437 437 GLU GLU A . n A 1 47 TRP 47 438 438 TRP TRP A . n A 1 48 ALA 48 439 439 ALA ALA A . n A 1 49 HIS 49 440 440 HIS HIS A . n A 1 50 MSE 50 441 441 MSE MSE A . n A 1 51 LEU 51 442 442 LEU LEU A . n A 1 52 ALA 52 443 443 ALA ALA A . n A 1 53 LEU 53 444 444 LEU LEU A . n A 1 54 ASN 54 445 445 ASN ASN A . n A 1 55 PRO 55 446 446 PRO PRO A . n A 1 56 GLU 56 447 447 GLU GLU A . n A 1 57 ARG 57 448 448 ARG ARG A . n A 1 58 LYS 58 449 449 LYS LYS A . n A 1 59 ASP 59 450 450 ASP ASP A . n A 1 60 PHE 60 451 451 PHE PHE A . n A 1 61 LEU 61 452 452 LEU LEU A . n A 1 62 TRP 62 453 453 TRP TRP A . n A 1 63 LYS 63 454 454 LYS LYS A . n A 1 64 ASN 64 455 455 ASN ASN A . n A 1 65 GLN 65 456 456 GLN GLN A . n A 1 66 SER 66 457 457 SER SER A . n A 1 67 GLU 67 458 458 GLU GLU A . n A 1 68 MSE 68 459 459 MSE MSE A . n A 1 69 ASN 69 460 460 ASN ASN A . n A 1 70 SER 70 461 461 SER SER A . n A 1 71 ALA 71 462 462 ALA ALA A . n A 1 72 PHE 72 463 463 PHE PHE A . n A 1 73 PHE 73 464 464 PHE PHE A . n A 1 74 ASP 74 465 465 ASP ASP A . n A 1 75 LEU 75 466 466 LEU LEU A . n A 1 76 CYS 76 467 467 CYS CYS A . n A 1 77 GLU 77 468 468 GLU GLU A . n A 1 78 VAL 78 469 469 VAL VAL A . n A 1 79 GLY 79 470 470 GLY GLY A . n A 1 80 LYS 80 471 471 LYS LYS A . n A 1 81 GLN 81 472 472 GLN GLN A . n A 1 82 VAL 82 473 473 VAL VAL A . n A 1 83 MSE 83 474 474 MSE MSE A . n A 1 84 LEU 84 475 475 LEU LEU A . n A 1 85 GLY 85 476 476 GLY GLY A . n A 1 86 LEU 86 477 477 LEU LEU A . n A 1 87 LEU 87 478 478 LEU LEU A . n A 1 88 GLY 88 479 479 GLY GLY A . n A 1 89 LYS 89 480 480 LYS LYS A . n A 1 90 GLU 90 481 481 GLU GLU A . n A 1 91 VAL 91 482 482 VAL VAL A . n A 1 92 ALA 92 483 483 ALA ALA A . n A 1 93 LEU 93 484 484 LEU LEU A . n A 1 94 PRO 94 485 485 PRO PRO A . n A 1 95 LYS 95 486 486 LYS LYS A . n A 1 96 GLU 96 487 487 GLU GLU A . n A 1 97 GLU 97 488 488 GLU GLU A . n A 1 98 GLN 98 489 489 GLN GLN A . n A 1 99 ALA 99 490 490 ALA ALA A . n A 1 100 PHE 100 491 491 PHE PHE A . n A 1 101 TRP 101 492 492 TRP TRP A . n A 1 102 ILE 102 493 493 ILE ILE A . n A 1 103 MSE 103 494 494 MSE MSE A . n A 1 104 TYR 104 495 495 TYR TYR A . n A 1 105 ALA 105 496 496 ALA ALA A . n A 1 106 VAL 106 497 497 VAL VAL A . n A 1 107 HIS 107 498 498 HIS HIS A . n A 1 108 LEU 108 499 499 LEU LEU A . n A 1 109 SER 109 500 500 SER SER A . n A 1 110 ALA 110 501 501 ALA ALA A . n A 1 111 ALA 111 502 502 ALA ALA A . n A 1 112 CYS 112 503 503 CYS CYS A . n A 1 113 ALA 113 504 504 ALA ALA A . n A 1 114 GLU 114 505 505 GLU GLU A . n A 1 115 GLU 115 506 506 GLU GLU A . n A 1 116 LEU 116 507 507 LEU LEU A . n A 1 117 HIS 117 508 508 HIS HIS A . n A 1 118 MSE 118 509 509 MSE MSE A . n A 1 119 PRO 119 510 510 PRO PRO A . n A 1 120 GLU 120 511 511 GLU GLU A . n A 1 121 VAL 121 512 512 VAL VAL A . n A 1 122 ALA 122 513 513 ALA ALA A . n A 1 123 MSE 123 514 514 MSE MSE A . n A 1 124 SER 124 515 515 SER SER A . n A 1 125 LEU 125 516 516 LEU LEU A . n A 1 126 ARG 126 517 517 ARG ARG A . n A 1 127 LYS 127 518 518 LYS LYS A . n A 1 128 LEU 128 519 519 LEU LEU A . n A 1 129 ASN 129 520 520 ASN ASN A . n A 1 130 VAL 130 521 521 VAL VAL A . n A 1 131 LYS 131 522 522 LYS LYS A . n A 1 132 LEU 132 523 523 LEU LEU A . n A 1 133 LYS 133 524 524 LYS LYS A . n A 1 134 ASP 134 525 525 ASP ASP A . n A 1 135 PHE 135 526 526 PHE PHE A . n A 1 136 ASN 136 527 527 ASN ASN A . n A 1 137 PHE 137 528 528 PHE PHE A . n A 1 138 GLY 138 529 529 GLY GLY A . n A 1 139 GLY 139 530 ? ? ? A . n A 1 140 THR 140 531 ? ? ? A . n A 1 141 ARG 141 532 ? ? ? A . n A 1 142 TYR 142 533 ? ? ? A . n A 1 143 PHE 143 534 ? ? ? A . n A 1 144 LYS 144 535 ? ? ? A . n A 1 145 ASP 145 536 536 ASP ASP A . n A 1 146 MSE 146 537 537 MSE MSE A . n A 1 147 PRO 147 538 538 PRO PRO A . n A 1 148 PRO 148 539 539 PRO PRO A . n A 1 149 GLU 149 540 540 GLU GLU A . n A 1 150 GLU 150 541 541 GLU GLU A . n A 1 151 LYS 151 542 542 LYS LYS A . n A 1 152 LYS 152 543 543 LYS LYS A . n A 1 153 ARG 153 544 544 ARG ARG A . n A 1 154 ARG 154 545 545 ARG ARG A . n A 1 155 MSE 155 546 546 MSE MSE A . n A 1 156 GLU 156 547 547 GLU GLU A . n A 1 157 ARG 157 548 548 ARG ARG A . n A 1 158 LYS 158 549 549 LYS LYS A . n A 1 159 GLN 159 550 550 GLN GLN A . n A 1 160 ARG 160 551 551 ARG ARG A . n A 1 161 ILE 161 552 552 ILE ILE A . n A 1 162 GLU 162 553 553 GLU GLU A . n A 1 163 GLU 163 554 554 GLU GLU A . n A 1 164 ALA 164 555 555 ALA ALA A . n A 1 165 ARG 165 556 556 ARG ARG A . n A 1 166 ARG 166 557 557 ARG ARG A . n A 1 167 HIS 167 558 558 HIS HIS A . n A 1 168 GLY 168 559 559 GLY GLY A . n A 1 169 MSE 169 560 560 MSE MSE A . n A 1 170 PRO 170 561 561 PRO PRO 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 B 2 NO3 1 1562 1562 NO3 NO3 A . C 3 GOL 1 1563 1563 GOL GOL A . D 4 HOH 1 2001 2001 HOH HOH A . D 4 HOH 2 2002 2002 HOH HOH A . D 4 HOH 3 2003 2003 HOH HOH A . D 4 HOH 4 2004 2004 HOH HOH A . D 4 HOH 5 2005 2005 HOH HOH A . D 4 HOH 6 2006 2006 HOH HOH A . D 4 HOH 7 2007 2007 HOH HOH A . D 4 HOH 8 2008 2008 HOH HOH A . D 4 HOH 9 2009 2009 HOH HOH A . D 4 HOH 10 2010 2010 HOH HOH A . D 4 HOH 11 2011 2011 HOH HOH A . D 4 HOH 12 2012 2012 HOH HOH A . D 4 HOH 13 2013 2013 HOH HOH A . D 4 HOH 14 2014 2014 HOH HOH A . D 4 HOH 15 2015 2015 HOH HOH A . D 4 HOH 16 2016 2016 HOH HOH A . D 4 HOH 17 2017 2017 HOH HOH A . D 4 HOH 18 2018 2018 HOH HOH A . D 4 HOH 19 2019 2019 HOH HOH A . D 4 HOH 20 2020 2020 HOH HOH A . D 4 HOH 21 2021 2021 HOH HOH A . D 4 HOH 22 2022 2022 HOH HOH A . D 4 HOH 23 2023 2023 HOH HOH A . D 4 HOH 24 2024 2024 HOH HOH A . D 4 HOH 25 2025 2025 HOH HOH A . D 4 HOH 26 2026 2026 HOH HOH A . D 4 HOH 27 2027 2027 HOH HOH A . D 4 HOH 28 2028 2028 HOH HOH A . D 4 HOH 29 2029 2029 HOH HOH A . D 4 HOH 30 2030 2030 HOH HOH A . D 4 HOH 31 2031 2031 HOH HOH A . D 4 HOH 32 2032 2032 HOH HOH A . D 4 HOH 33 2033 2033 HOH HOH A . D 4 HOH 34 2034 2034 HOH HOH A . D 4 HOH 35 2035 2035 HOH HOH A . D 4 HOH 36 2036 2036 HOH HOH A . D 4 HOH 37 2037 2037 HOH HOH A . D 4 HOH 38 2038 2038 HOH HOH A . D 4 HOH 39 2039 2039 HOH HOH A . D 4 HOH 40 2040 2040 HOH HOH A . D 4 HOH 41 2041 2041 HOH HOH A . D 4 HOH 42 2042 2042 HOH HOH A . D 4 HOH 43 2043 2043 HOH HOH A . D 4 HOH 44 2044 2044 HOH HOH A . D 4 HOH 45 2045 2045 HOH HOH A . D 4 HOH 46 2046 2046 HOH HOH A . D 4 HOH 47 2047 2047 HOH HOH A . D 4 HOH 48 2048 2048 HOH HOH A . D 4 HOH 49 2049 2049 HOH HOH A . D 4 HOH 50 2050 2050 HOH HOH A . D 4 HOH 51 2051 2051 HOH HOH A . D 4 HOH 52 2052 2052 HOH HOH A . D 4 HOH 53 2053 2053 HOH HOH A . D 4 HOH 54 2054 2054 HOH HOH A . D 4 HOH 55 2055 2055 HOH HOH A . D 4 HOH 56 2056 2056 HOH HOH A . D 4 HOH 57 2057 2057 HOH HOH A . D 4 HOH 58 2058 2058 HOH HOH A . D 4 HOH 59 2059 2059 HOH HOH A . D 4 HOH 60 2060 2060 HOH HOH A . D 4 HOH 61 2061 2061 HOH HOH A . D 4 HOH 62 2062 2062 HOH HOH A . D 4 HOH 63 2063 2063 HOH HOH A . D 4 HOH 64 2064 2064 HOH HOH A . D 4 HOH 65 2065 2065 HOH HOH A . D 4 HOH 66 2066 2066 HOH HOH A . D 4 HOH 67 2067 2067 HOH HOH A . D 4 HOH 68 2068 2068 HOH HOH A . D 4 HOH 69 2069 2069 HOH HOH A . D 4 HOH 70 2070 2070 HOH HOH A . D 4 HOH 71 2071 2071 HOH HOH A . D 4 HOH 72 2072 2072 HOH HOH A . D 4 HOH 73 2073 2073 HOH HOH A . D 4 HOH 74 2074 2074 HOH HOH A . D 4 HOH 75 2075 2075 HOH HOH A . D 4 HOH 76 2076 2076 HOH HOH A . D 4 HOH 77 2077 2077 HOH HOH A . D 4 HOH 78 2078 2078 HOH HOH A . D 4 HOH 79 2079 2079 HOH HOH A . D 4 HOH 80 2080 2080 HOH HOH A . D 4 HOH 81 2081 2081 HOH HOH A . D 4 HOH 82 2082 2082 HOH HOH A . D 4 HOH 83 2083 2083 HOH HOH A . D 4 HOH 84 2084 2084 HOH HOH A . D 4 HOH 85 2085 2085 HOH HOH A . D 4 HOH 86 2086 2086 HOH HOH A . D 4 HOH 87 2087 2087 HOH HOH A . D 4 HOH 88 2088 2088 HOH HOH A . D 4 HOH 89 2089 2089 HOH HOH A . D 4 HOH 90 2090 2090 HOH HOH A . D 4 HOH 91 2091 2091 HOH HOH A . D 4 HOH 92 2092 2092 HOH HOH A . D 4 HOH 93 2093 2093 HOH HOH A . D 4 HOH 94 2094 2094 HOH HOH A . D 4 HOH 95 2095 2095 HOH HOH A . D 4 HOH 96 2096 2096 HOH HOH A . D 4 HOH 97 2097 2097 HOH HOH A . D 4 HOH 98 2098 2098 HOH HOH A . D 4 HOH 99 2099 2099 HOH HOH A . D 4 HOH 100 2100 2100 HOH HOH A . D 4 HOH 101 2101 2101 HOH HOH A . D 4 HOH 102 2102 2102 HOH HOH A . D 4 HOH 103 2103 2103 HOH HOH A . D 4 HOH 104 2104 2104 HOH HOH A . D 4 HOH 105 2105 2105 HOH HOH A . D 4 HOH 106 2106 2106 HOH HOH A . D 4 HOH 107 2107 2107 HOH HOH A . D 4 HOH 108 2108 2108 HOH HOH A . D 4 HOH 109 2109 2109 HOH HOH A . D 4 HOH 110 2110 2110 HOH HOH A . D 4 HOH 111 2111 2111 HOH HOH A . D 4 HOH 112 2112 2112 HOH HOH A . D 4 HOH 113 2113 2113 HOH HOH A . D 4 HOH 114 2114 2114 HOH HOH A . D 4 HOH 115 2115 2115 HOH HOH A . D 4 HOH 116 2116 2116 HOH HOH A . D 4 HOH 117 2117 2117 HOH HOH A . D 4 HOH 118 2118 2118 HOH HOH A . D 4 HOH 119 2119 2119 HOH HOH A . D 4 HOH 120 2120 2120 HOH HOH A . D 4 HOH 121 2121 2121 HOH HOH A . D 4 HOH 122 2122 2122 HOH HOH A . D 4 HOH 123 2123 2123 HOH HOH A . D 4 HOH 124 2124 2124 HOH HOH A . D 4 HOH 125 2125 2125 HOH HOH A . D 4 HOH 126 2126 2126 HOH HOH A . D 4 HOH 127 2127 2127 HOH HOH A . D 4 HOH 128 2128 2128 HOH HOH A . D 4 HOH 129 2129 2129 HOH HOH A . D 4 HOH 130 2130 2130 HOH HOH A . D 4 HOH 131 2131 2131 HOH HOH A . D 4 HOH 132 2132 2132 HOH HOH A . D 4 HOH 133 2133 2133 HOH HOH A . D 4 HOH 134 2134 2134 HOH HOH A . D 4 HOH 135 2135 2135 HOH HOH A . D 4 HOH 136 2136 2136 HOH HOH A . D 4 HOH 137 2137 2137 HOH HOH A . D 4 HOH 138 2138 2138 HOH HOH A . D 4 HOH 139 2139 2139 HOH HOH A . D 4 HOH 140 2140 2140 HOH HOH A . D 4 HOH 141 2141 2141 HOH HOH A . D 4 HOH 142 2142 2142 HOH HOH A . D 4 HOH 143 2143 2143 HOH HOH A . D 4 HOH 144 2144 2144 HOH HOH A . D 4 HOH 145 2145 2145 HOH HOH A . D 4 HOH 146 2146 2146 HOH HOH A . D 4 HOH 147 2147 2147 HOH HOH A . D 4 HOH 148 2148 2148 HOH HOH A . D 4 HOH 149 2149 2149 HOH HOH A . D 4 HOH 150 2150 2150 HOH HOH A . D 4 HOH 151 2151 2151 HOH HOH A . D 4 HOH 152 2152 2152 HOH HOH A . D 4 HOH 153 2153 2153 HOH HOH A . D 4 HOH 154 2154 2154 HOH HOH A . D 4 HOH 155 2155 2155 HOH HOH A . D 4 HOH 156 2156 2156 HOH HOH A . D 4 HOH 157 2157 2157 HOH HOH A . D 4 HOH 158 2158 2158 HOH HOH A . D 4 HOH 159 2159 2159 HOH HOH A . D 4 HOH 160 2160 2160 HOH HOH A . D 4 HOH 161 2161 2161 HOH HOH A . D 4 HOH 162 2162 2162 HOH HOH A . D 4 HOH 163 2163 2163 HOH HOH A . D 4 HOH 164 2164 2164 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 4 A MSE 395 ? MET SELENOMETHIONINE 2 A MSE 31 A MSE 422 ? MET SELENOMETHIONINE 3 A MSE 50 A MSE 441 ? MET SELENOMETHIONINE 4 A MSE 68 A MSE 459 ? MET SELENOMETHIONINE 5 A MSE 83 A MSE 474 ? MET SELENOMETHIONINE 6 A MSE 103 A MSE 494 ? MET SELENOMETHIONINE 7 A MSE 118 A MSE 509 ? MET SELENOMETHIONINE 8 A MSE 123 A MSE 514 ? MET SELENOMETHIONINE 9 A MSE 146 A MSE 537 ? MET SELENOMETHIONINE 10 A MSE 155 A MSE 546 ? MET SELENOMETHIONINE 11 A MSE 169 A MSE 560 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-03-30 2 'Structure model' 1 1 2011-08-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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 2 'Structure model' 'Non-polymer description' 3 2 'Structure model' 'Version format compliance' # 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[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] 'X-RAY DIFFRACTION' 1 ? refined -13.9927 51.6852 37.5633 0.0397 0.0324 0.0283 0.0100 -0.0227 -0.0242 1.6651 1.0240 1.3323 0.0467 0.5239 0.0857 -0.0095 -0.0279 0.0879 0.0350 -0.0704 0.0165 -0.0247 -0.0248 0.0799 'X-RAY DIFFRACTION' 2 ? refined -20.0759 40.8473 26.0444 0.0407 0.0505 0.0358 0.0134 -0.0328 -0.0251 1.0133 1.7000 1.3267 0.5696 0.4810 0.6454 0.0329 0.0202 -0.0340 -0.0382 -0.0015 -0.0500 0.0558 -0.0423 -0.0314 'X-RAY DIFFRACTION' 3 ? refined -9.0062 55.2227 16.5086 0.3435 0.5471 0.1048 -0.1921 -0.0228 0.1916 6.6509 9.6501 22.9384 0.9368 -9.8369 1.8308 -0.7185 1.1977 0.1743 -1.5041 0.2648 -0.2681 0.2249 -0.2272 0.4537 'X-RAY DIFFRACTION' 4 ? refined -29.9645 31.5693 19.6728 0.0964 0.1099 0.0949 0.0039 -0.0260 0.0064 0.1733 2.6997 1.0013 0.0225 0.2976 -1.0846 0.0250 -0.0563 0.0776 0.1671 -0.1264 0.1196 -0.0066 -0.0053 0.1014 # 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.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.selection_details 'X-RAY DIFFRACTION' 1 1 A 395 ? ? A 426 ? ? ? ? 'X-RAY DIFFRACTION' 2 1 A 467 ? ? A 495 ? ? ? ? 'X-RAY DIFFRACTION' 3 1 A 549 ? ? A 561 ? ? ? ? 'X-RAY DIFFRACTION' 4 2 A 427 ? ? A 437 ? ? ? ? 'X-RAY DIFFRACTION' 5 2 A 452 ? ? A 466 ? ? ? ? 'X-RAY DIFFRACTION' 6 2 A 496 ? ? A 529 ? ? ? ? 'X-RAY DIFFRACTION' 7 3 A 536 ? ? A 548 ? ? ? ? 'X-RAY DIFFRACTION' 8 4 A 438 ? ? A 451 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal XDS 'data reduction' . ? 1 SCALA 'data scaling' . ? 2 PHENIX.HYSS phasing . ? 3 PHASER phasing . ? 4 REFMAC refinement 5.6.0081 ? 5 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LYS A 402 ? ? -69.68 4.68 2 1 HIS A 413 ? ? 75.65 -5.88 3 1 MSE A 514 ? ? -105.40 78.69 # 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 A GLY 529 ? CA ? A GLY 138 CA 2 1 Y 1 A GLY 529 ? C ? A GLY 138 C 3 1 Y 1 A GLY 529 ? O ? A GLY 138 O # 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 THR 392 ? A THR 1 2 1 Y 1 A ASN 393 ? A ASN 2 3 1 Y 1 A LEU 394 ? A LEU 3 4 1 Y 1 A GLY 530 ? A GLY 139 5 1 Y 1 A THR 531 ? A THR 140 6 1 Y 1 A ARG 532 ? A ARG 141 7 1 Y 1 A TYR 533 ? A TYR 142 8 1 Y 1 A PHE 534 ? A PHE 143 9 1 Y 1 A LYS 535 ? A LYS 144 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NITRATE ION' NO3 3 GLYCEROL GOL 4 water HOH #