data_1WFX # _entry.id 1WFX # _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 1WFX RCSB RCSB023536 WWPDB D_1000023536 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id ape001000204 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1WFX _pdbx_database_status.recvd_initial_deposition_date 2004-05-27 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kato-Murayama, M.' 1 'Bessho, Y.' 2 'Shirouzu, M.' 3 'Yokoyama, S.' 4 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 5 # _citation.id primary _citation.title ;Crystal Structure of the RNA 2'-Phosphotransferase from Aeropyrum pernix K1 ; _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 348 _citation.page_first 295 _citation.page_last 305 _citation.year 2005 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15811369 _citation.pdbx_database_id_DOI 10.1016/j.jmb.2005.02.049 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Kato-Murayama, M.' 1 primary 'Bessho, Y.' 2 primary 'Shirouzu, M.' 3 primary 'Yokoyama, S.' 4 # _cell.entry_id 1WFX _cell.length_a 102.667 _cell.length_b 102.667 _cell.length_c 101.489 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WFX _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man ;Probable RNA 2'-phosphotransferase ; 21398.234 1 2.7.-.- ? 'RESIDUES 1-186' ? 2 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 5 ? ? ? ? 4 water nat water 18.015 16 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;RNA 2'-phosphotransferase, APE0204 protein ; # _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 ;(MSE)RVRLSKTLAGILRHHPGRYGVRLTREGWARVSEVVEGLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYG HSIPVNVEPLPGEPPPILYHGTTEEALPLI(MSE)ERGI(MSE)RGRRLKVHLTSSLEDAVSTGRRHGNLVAVLLVDVEC LRRRGLKVER(MSE)SKTVYTVDWVPPECIAEVRRESLGRSL ; _entity_poly.pdbx_seq_one_letter_code_can ;MRVRLSKTLAGILRHHPGRYGVRLTREGWARVSEVVEGLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHSIP VNVEPLPGEPPPILYHGTTEEALPLIMERGIMRGRRLKVHLTSSLEDAVSTGRRHGNLVAVLLVDVECLRRRGLKVERMS KTVYTVDWVPPECIAEVRRESLGRSL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ape001000204 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MSE n 1 2 ARG n 1 3 VAL n 1 4 ARG n 1 5 LEU n 1 6 SER n 1 7 LYS n 1 8 THR n 1 9 LEU n 1 10 ALA n 1 11 GLY n 1 12 ILE n 1 13 LEU n 1 14 ARG n 1 15 HIS n 1 16 HIS n 1 17 PRO n 1 18 GLY n 1 19 ARG n 1 20 TYR n 1 21 GLY n 1 22 VAL n 1 23 ARG n 1 24 LEU n 1 25 THR n 1 26 ARG n 1 27 GLU n 1 28 GLY n 1 29 TRP n 1 30 ALA n 1 31 ARG n 1 32 VAL n 1 33 SER n 1 34 GLU n 1 35 VAL n 1 36 VAL n 1 37 GLU n 1 38 GLY n 1 39 LEU n 1 40 ARG n 1 41 LYS n 1 42 ALA n 1 43 GLY n 1 44 TRP n 1 45 SER n 1 46 TRP n 1 47 VAL n 1 48 GLU n 1 49 GLU n 1 50 TRP n 1 51 HIS n 1 52 ILE n 1 53 VAL n 1 54 GLY n 1 55 VAL n 1 56 ALA n 1 57 LEU n 1 58 HIS n 1 59 ASP n 1 60 PRO n 1 61 LYS n 1 62 GLY n 1 63 ARG n 1 64 TYR n 1 65 GLU n 1 66 LEU n 1 67 ARG n 1 68 ASN n 1 69 GLY n 1 70 GLU n 1 71 ILE n 1 72 ARG n 1 73 ALA n 1 74 ARG n 1 75 TYR n 1 76 GLY n 1 77 HIS n 1 78 SER n 1 79 ILE n 1 80 PRO n 1 81 VAL n 1 82 ASN n 1 83 VAL n 1 84 GLU n 1 85 PRO n 1 86 LEU n 1 87 PRO n 1 88 GLY n 1 89 GLU n 1 90 PRO n 1 91 PRO n 1 92 PRO n 1 93 ILE n 1 94 LEU n 1 95 TYR n 1 96 HIS n 1 97 GLY n 1 98 THR n 1 99 THR n 1 100 GLU n 1 101 GLU n 1 102 ALA n 1 103 LEU n 1 104 PRO n 1 105 LEU n 1 106 ILE n 1 107 MSE n 1 108 GLU n 1 109 ARG n 1 110 GLY n 1 111 ILE n 1 112 MSE n 1 113 ARG n 1 114 GLY n 1 115 ARG n 1 116 ARG n 1 117 LEU n 1 118 LYS n 1 119 VAL n 1 120 HIS n 1 121 LEU n 1 122 THR n 1 123 SER n 1 124 SER n 1 125 LEU n 1 126 GLU n 1 127 ASP n 1 128 ALA n 1 129 VAL n 1 130 SER n 1 131 THR n 1 132 GLY n 1 133 ARG n 1 134 ARG n 1 135 HIS n 1 136 GLY n 1 137 ASN n 1 138 LEU n 1 139 VAL n 1 140 ALA n 1 141 VAL n 1 142 LEU n 1 143 LEU n 1 144 VAL n 1 145 ASP n 1 146 VAL n 1 147 GLU n 1 148 CYS n 1 149 LEU n 1 150 ARG n 1 151 ARG n 1 152 ARG n 1 153 GLY n 1 154 LEU n 1 155 LYS n 1 156 VAL n 1 157 GLU n 1 158 ARG n 1 159 MSE n 1 160 SER n 1 161 LYS n 1 162 THR n 1 163 VAL n 1 164 TYR n 1 165 THR n 1 166 VAL n 1 167 ASP n 1 168 TRP n 1 169 VAL n 1 170 PRO n 1 171 PRO n 1 172 GLU n 1 173 CYS n 1 174 ILE n 1 175 ALA n 1 176 GLU n 1 177 VAL n 1 178 ARG n 1 179 ARG n 1 180 GLU n 1 181 SER n 1 182 LEU n 1 183 GLY n 1 184 ARG n 1 185 SER n 1 186 LEU 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 Aeropyrum _entity_src_gen.pdbx_gene_src_gene APE0204 _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 'Aeropyrum pernix' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 56636 _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 Escherichia _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 ? _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 pET11a _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code KPTA_AERPE _struct_ref.pdbx_db_accession Q9YFP5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MRVRLSKTLAGILRHHPGRYGVRLTREGWARVSEVVEGLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHSIP VNVEPLPGEPPPILYHGTTEEALPLIMERGIMRGRRLKVHLTSSLEDAVSTGRRHGNLVAVLLVDVECLRRRGLKVERMS KTVYTVDWVPPECIAEVRRESLGRSL ; _struct_ref.pdbx_align_begin 35 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1WFX _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 186 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9YFP5 _struct_ref_seq.db_align_beg 35 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 220 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 186 # 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 1WFX MSE A 1 ? UNP Q9YFP5 MET 35 'MODIFIED RESIDUE' 1 1 1 1WFX MSE A 107 ? UNP Q9YFP5 MET 141 'MODIFIED RESIDUE' 107 2 1 1WFX MSE A 112 ? UNP Q9YFP5 MET 146 'MODIFIED RESIDUE' 112 3 1 1WFX MSE A 159 ? UNP Q9YFP5 MET 193 'MODIFIED RESIDUE' 159 4 # 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 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # _exptl.entry_id 1WFX _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.4 _exptl_crystal.density_percent_sol 49.0 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'RIGAKU JUPITER 210' _diffrn_detector.pdbx_collection_date 2004-04-06 _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 MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9789 1.0 2 0.9791 1.0 3 0.970 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL26B1' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL26B1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9789, 0.9791, 0.970' # _reflns.entry_id 1WFX _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 44.28 _reflns.d_resolution_high 2.80 _reflns.number_obs 5217 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 114.6 _reflns.pdbx_redundancy ? _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 # _reflns_shell.d_res_high 2.80 _reflns_shell.d_res_low 2.90 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1WFX _refine.ls_number_reflns_obs 5213 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 1574085.55 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 44.07 _refine.ls_d_res_high 2.80 _refine.ls_percent_reflns_obs 99.8 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.22 _refine.ls_R_factor_R_free 0.286 _refine.ls_R_factor_R_free_error 0.012 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.3 _refine.ls_number_reflns_R_free 536 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 29.0 _refine.aniso_B[1][1] -0.13 _refine.aniso_B[2][2] -0.13 _refine.aniso_B[3][3] 0.27 _refine.aniso_B[1][2] 3.89 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.388121 _refine.solvent_model_param_bsol 42.0314 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1WFX _refine_analyze.Luzzati_coordinate_error_obs 0.32 _refine_analyze.Luzzati_sigma_a_obs 0.38 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.47 _refine_analyze.Luzzati_sigma_a_free 0.61 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1442 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 16 _refine_hist.number_atoms_total 1464 _refine_hist.d_res_high 2.80 _refine_hist.d_res_low 44.07 # 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 c_bond_d 0.007 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.4 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 22.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.93 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.80 _refine_ls_shell.d_res_low 2.98 _refine_ls_shell.number_reflns_R_work 775 _refine_ls_shell.R_factor_R_work 0.298 _refine_ls_shell.percent_reflns_obs 100.0 _refine_ls_shell.R_factor_R_free 0.418 _refine_ls_shell.R_factor_R_free_error 0.048 _refine_ls_shell.percent_reflns_R_free 8.8 _refine_ls_shell.number_reflns_R_free 75 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 WATER_REP.PARAM WATER_REP.TOP 'X-RAY DIFFRACTION' 3 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' # _struct.entry_id 1WFX _struct.title 'Crystal Structure of APE0204 from Aeropyrum pernix' _struct.pdbx_descriptor ;Probable RNA 2'-phosphotransferase(E.C.2.7.-.-) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1WFX _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text ;RNA 2'-phosphotransferase, tRNA splicing, NAD, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, transferase ; # 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 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 4 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 ARG A 4 ? HIS A 15 ? ARG A 4 HIS A 15 1 ? 12 HELX_P HELX_P2 2 PRO A 17 ? GLY A 21 ? PRO A 17 GLY A 21 5 ? 5 HELX_P HELX_P3 3 VAL A 32 ? ALA A 42 ? VAL A 32 ALA A 42 1 ? 11 HELX_P HELX_P4 4 GLU A 48 ? ASP A 59 ? GLU A 48 ASP A 59 1 ? 12 HELX_P HELX_P5 5 THR A 99 ? GLU A 101 ? THR A 99 GLU A 101 5 ? 3 HELX_P HELX_P6 6 ALA A 102 ? GLY A 110 ? ALA A 102 GLY A 110 1 ? 9 HELX_P HELX_P7 7 SER A 124 ? ARG A 133 ? SER A 124 ARG A 133 1 ? 10 HELX_P HELX_P8 8 VAL A 146 ? ARG A 152 ? VAL A 146 ARG A 152 1 ? 7 HELX_P HELX_P9 9 PRO A 170 ? GLU A 172 ? PRO A 170 GLU A 172 5 ? 3 # _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 disulf1 disulf ? ? A CYS 148 SG ? ? ? 1_555 A CYS 173 SG ? ? A CYS 148 A CYS 173 1_555 ? ? ? ? ? ? ? 2.044 ? covale1 covale ? ? A ILE 106 C ? ? ? 1_555 A MSE 107 N ? ? A ILE 106 A MSE 107 1_555 ? ? ? ? ? ? ? 1.325 ? covale2 covale ? ? A MSE 107 C ? ? ? 1_555 A GLU 108 N ? ? A MSE 107 A GLU 108 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A ILE 111 C ? ? ? 1_555 A MSE 112 N ? ? A ILE 111 A MSE 112 1_555 ? ? ? ? ? ? ? 1.329 ? covale4 covale ? ? A MSE 112 C ? ? ? 1_555 A ARG 113 N ? ? A MSE 112 A ARG 113 1_555 ? ? ? ? ? ? ? 1.332 ? covale5 covale ? ? A ARG 158 C ? ? ? 1_555 A MSE 159 N ? ? A ARG 158 A MSE 159 1_555 ? ? ? ? ? ? ? 1.329 ? covale6 covale ? ? A MSE 159 C ? ? ? 1_555 A SER 160 N ? ? A MSE 159 A SER 160 1_555 ? ? ? ? ? ? ? 1.330 ? metalc1 metalc ? ? B ZN . ZN ? ? ? 1_555 H HOH . O ? ? A ZN 201 A HOH 316 1_555 ? ? ? ? ? ? ? 2.054 ? metalc2 metalc ? ? B ZN . ZN ? ? ? 1_555 A HIS 58 NE2 ? ? A ZN 201 A HIS 58 1_555 ? ? ? ? ? ? ? 2.188 ? metalc3 metalc ? ? B ZN . ZN ? ? ? 1_555 H HOH . O ? ? A ZN 201 A HOH 316 2_665 ? ? ? ? ? ? ? 2.055 ? metalc4 metalc ? ? B ZN . ZN ? ? ? 1_555 H HOH . O ? ? A ZN 201 A HOH 316 3_565 ? ? ? ? ? ? ? 2.054 ? metalc5 metalc ? ? B ZN . ZN ? ? ? 1_555 A HIS 58 NE2 ? ? A ZN 201 A HIS 58 2_665 ? ? ? ? ? ? ? 2.217 ? metalc6 metalc ? ? B ZN . ZN ? ? ? 1_555 A HIS 58 NE2 ? ? A ZN 201 A HIS 58 3_565 ? ? ? ? ? ? ? 2.215 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? metalc ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 3 ? B ? 3 ? C ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ALA A 30 ? ARG A 31 ? ALA A 30 ARG A 31 A 2 GLU A 70 ? ALA A 73 ? GLU A 70 ALA A 73 A 3 TYR A 64 ? ARG A 67 ? TYR A 64 ARG A 67 B 1 ILE A 93 ? HIS A 96 ? ILE A 93 HIS A 96 B 2 ALA A 140 ? ASP A 145 ? ALA A 140 ASP A 145 B 3 ILE A 174 ? ARG A 179 ? ILE A 174 ARG A 179 C 1 VAL A 119 ? THR A 122 ? VAL A 119 THR A 122 C 2 VAL A 163 ? VAL A 166 ? VAL A 163 VAL A 166 C 3 GLU A 157 ? ARG A 158 ? GLU A 157 ARG A 158 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N ALA A 30 ? N ALA A 30 O ILE A 71 ? O ILE A 71 A 2 3 O GLU A 70 ? O GLU A 70 N ARG A 67 ? N ARG A 67 B 1 2 N LEU A 94 ? N LEU A 94 O VAL A 144 ? O VAL A 144 B 2 3 N LEU A 143 ? N LEU A 143 O GLU A 176 ? O GLU A 176 C 1 2 N LEU A 121 ? N LEU A 121 O TYR A 164 ? O TYR A 164 C 2 3 O THR A 165 ? O THR A 165 N GLU A 157 ? N GLU A 157 # 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 ? ? ? ? 6 'BINDING SITE FOR RESIDUE ZN A 201' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE CL A 202' AC3 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE CL A 203' AC4 Software ? ? ? ? 2 'BINDING SITE FOR RESIDUE CL A 204' AC5 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE CL A 206' # 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 6 HIS A 58 ? HIS A 58 . ? 1_555 ? 2 AC1 6 HIS A 58 ? HIS A 58 . ? 2_665 ? 3 AC1 6 HIS A 58 ? HIS A 58 . ? 3_565 ? 4 AC1 6 HOH H . ? HOH A 316 . ? 3_565 ? 5 AC1 6 HOH H . ? HOH A 316 . ? 2_665 ? 6 AC1 6 HOH H . ? HOH A 316 . ? 1_555 ? 7 AC2 3 ARG A 14 ? ARG A 14 . ? 1_555 ? 8 AC2 3 LYS A 61 ? LYS A 61 . ? 1_555 ? 9 AC2 3 ARG A 63 ? ARG A 63 . ? 1_555 ? 10 AC3 1 ARG A 150 ? ARG A 150 . ? 15_554 ? 11 AC4 2 HIS A 15 ? HIS A 15 . ? 1_555 ? 12 AC4 2 ARG A 115 ? ARG A 115 . ? 1_555 ? 13 AC5 1 ARG A 158 ? ARG A 158 . ? 1_555 ? # _database_PDB_matrix.entry_id 1WFX _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 1WFX _atom_sites.fract_transf_matrix[1][1] 0.009740 _atom_sites.fract_transf_matrix[1][2] 0.005624 _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] 0.011247 _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] 0.009853 _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 CL N O S SE ZN # 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 MSE 1 1 ? ? ? A . n A 1 2 ARG 2 2 ? ? ? A . n A 1 3 VAL 3 3 3 VAL VAL A . n A 1 4 ARG 4 4 4 ARG ARG A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 LYS 7 7 7 LYS LYS A . n A 1 8 THR 8 8 8 THR THR A . n A 1 9 LEU 9 9 9 LEU LEU A . n A 1 10 ALA 10 10 10 ALA ALA A . n A 1 11 GLY 11 11 11 GLY GLY A . n A 1 12 ILE 12 12 12 ILE ILE A . n A 1 13 LEU 13 13 13 LEU LEU A . n A 1 14 ARG 14 14 14 ARG ARG A . n A 1 15 HIS 15 15 15 HIS HIS A . n A 1 16 HIS 16 16 16 HIS HIS A . n A 1 17 PRO 17 17 17 PRO PRO A . n A 1 18 GLY 18 18 18 GLY GLY A . n A 1 19 ARG 19 19 19 ARG ARG A . n A 1 20 TYR 20 20 20 TYR TYR A . n A 1 21 GLY 21 21 21 GLY GLY A . n A 1 22 VAL 22 22 22 VAL VAL A . n A 1 23 ARG 23 23 23 ARG ARG A . n A 1 24 LEU 24 24 24 LEU LEU A . n A 1 25 THR 25 25 25 THR THR A . n A 1 26 ARG 26 26 26 ARG ARG A . n A 1 27 GLU 27 27 27 GLU GLU A . n A 1 28 GLY 28 28 28 GLY GLY A . n A 1 29 TRP 29 29 29 TRP TRP A . n A 1 30 ALA 30 30 30 ALA ALA A . n A 1 31 ARG 31 31 31 ARG ARG A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 SER 33 33 33 SER SER A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 VAL 35 35 35 VAL VAL A . n A 1 36 VAL 36 36 36 VAL VAL A . n A 1 37 GLU 37 37 37 GLU GLU A . n A 1 38 GLY 38 38 38 GLY GLY A . n A 1 39 LEU 39 39 39 LEU LEU A . n A 1 40 ARG 40 40 40 ARG ARG A . n A 1 41 LYS 41 41 41 LYS LYS A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 GLY 43 43 43 GLY GLY A . n A 1 44 TRP 44 44 44 TRP TRP A . n A 1 45 SER 45 45 45 SER SER A . n A 1 46 TRP 46 46 46 TRP TRP A . n A 1 47 VAL 47 47 47 VAL VAL A . n A 1 48 GLU 48 48 48 GLU GLU A . n A 1 49 GLU 49 49 49 GLU GLU A . n A 1 50 TRP 50 50 50 TRP TRP A . n A 1 51 HIS 51 51 51 HIS HIS A . n A 1 52 ILE 52 52 52 ILE ILE A . n A 1 53 VAL 53 53 53 VAL VAL A . n A 1 54 GLY 54 54 54 GLY GLY A . n A 1 55 VAL 55 55 55 VAL VAL A . n A 1 56 ALA 56 56 56 ALA ALA A . n A 1 57 LEU 57 57 57 LEU LEU A . n A 1 58 HIS 58 58 58 HIS HIS A . n A 1 59 ASP 59 59 59 ASP ASP A . n A 1 60 PRO 60 60 60 PRO PRO A . n A 1 61 LYS 61 61 61 LYS LYS A . n A 1 62 GLY 62 62 62 GLY GLY A . n A 1 63 ARG 63 63 63 ARG ARG A . n A 1 64 TYR 64 64 64 TYR TYR A . n A 1 65 GLU 65 65 65 GLU GLU A . n A 1 66 LEU 66 66 66 LEU LEU A . n A 1 67 ARG 67 67 67 ARG ARG A . n A 1 68 ASN 68 68 68 ASN ASN A . n A 1 69 GLY 69 69 69 GLY GLY A . n A 1 70 GLU 70 70 70 GLU GLU A . n A 1 71 ILE 71 71 71 ILE ILE A . n A 1 72 ARG 72 72 72 ARG ARG A . n A 1 73 ALA 73 73 73 ALA ALA A . n A 1 74 ARG 74 74 74 ARG ARG A . n A 1 75 TYR 75 75 75 TYR TYR A . n A 1 76 GLY 76 76 76 GLY GLY A . n A 1 77 HIS 77 77 77 HIS HIS A . n A 1 78 SER 78 78 78 SER SER A . n A 1 79 ILE 79 79 79 ILE ILE A . n A 1 80 PRO 80 80 80 PRO PRO A . n A 1 81 VAL 81 81 81 VAL VAL A . n A 1 82 ASN 82 82 82 ASN ASN A . n A 1 83 VAL 83 83 83 VAL VAL A . n A 1 84 GLU 84 84 84 GLU GLU A . n A 1 85 PRO 85 85 85 PRO PRO A . n A 1 86 LEU 86 86 86 LEU LEU A . n A 1 87 PRO 87 87 87 PRO PRO A . n A 1 88 GLY 88 88 88 GLY GLY A . n A 1 89 GLU 89 89 89 GLU GLU A . n A 1 90 PRO 90 90 90 PRO PRO A . n A 1 91 PRO 91 91 91 PRO PRO A . n A 1 92 PRO 92 92 92 PRO PRO A . n A 1 93 ILE 93 93 93 ILE ILE A . n A 1 94 LEU 94 94 94 LEU LEU A . n A 1 95 TYR 95 95 95 TYR TYR A . n A 1 96 HIS 96 96 96 HIS HIS A . n A 1 97 GLY 97 97 97 GLY GLY A . n A 1 98 THR 98 98 98 THR THR A . n A 1 99 THR 99 99 99 THR THR A . n A 1 100 GLU 100 100 100 GLU GLU A . n A 1 101 GLU 101 101 101 GLU GLU A . n A 1 102 ALA 102 102 102 ALA ALA A . n A 1 103 LEU 103 103 103 LEU LEU A . n A 1 104 PRO 104 104 104 PRO PRO A . n A 1 105 LEU 105 105 105 LEU LEU A . n A 1 106 ILE 106 106 106 ILE ILE A . n A 1 107 MSE 107 107 107 MSE MSE A . n A 1 108 GLU 108 108 108 GLU GLU A . n A 1 109 ARG 109 109 109 ARG ARG A . n A 1 110 GLY 110 110 110 GLY GLY A . n A 1 111 ILE 111 111 111 ILE ILE A . n A 1 112 MSE 112 112 112 MSE MSE A . n A 1 113 ARG 113 113 113 ARG ARG A . n A 1 114 GLY 114 114 114 GLY GLY A . n A 1 115 ARG 115 115 115 ARG ARG A . n A 1 116 ARG 116 116 116 ARG ARG A . n A 1 117 LEU 117 117 117 LEU LEU A . n A 1 118 LYS 118 118 118 LYS LYS A . n A 1 119 VAL 119 119 119 VAL VAL A . n A 1 120 HIS 120 120 120 HIS HIS A . n A 1 121 LEU 121 121 121 LEU LEU A . n A 1 122 THR 122 122 122 THR THR A . n A 1 123 SER 123 123 123 SER SER A . n A 1 124 SER 124 124 124 SER SER A . n A 1 125 LEU 125 125 125 LEU LEU A . n A 1 126 GLU 126 126 126 GLU GLU A . n A 1 127 ASP 127 127 127 ASP ASP A . n A 1 128 ALA 128 128 128 ALA ALA A . n A 1 129 VAL 129 129 129 VAL VAL A . n A 1 130 SER 130 130 130 SER SER A . n A 1 131 THR 131 131 131 THR THR A . n A 1 132 GLY 132 132 132 GLY GLY A . n A 1 133 ARG 133 133 133 ARG ARG A . n A 1 134 ARG 134 134 134 ARG ARG A . n A 1 135 HIS 135 135 135 HIS HIS A . n A 1 136 GLY 136 136 136 GLY GLY A . n A 1 137 ASN 137 137 137 ASN ASN A . n A 1 138 LEU 138 138 138 LEU LEU A . n A 1 139 VAL 139 139 139 VAL VAL A . n A 1 140 ALA 140 140 140 ALA ALA A . n A 1 141 VAL 141 141 141 VAL VAL A . n A 1 142 LEU 142 142 142 LEU LEU A . n A 1 143 LEU 143 143 143 LEU LEU A . n A 1 144 VAL 144 144 144 VAL VAL A . n A 1 145 ASP 145 145 145 ASP ASP A . n A 1 146 VAL 146 146 146 VAL VAL A . n A 1 147 GLU 147 147 147 GLU GLU A . n A 1 148 CYS 148 148 148 CYS CYS A . n A 1 149 LEU 149 149 149 LEU LEU A . n A 1 150 ARG 150 150 150 ARG ARG A . n A 1 151 ARG 151 151 151 ARG ARG A . n A 1 152 ARG 152 152 152 ARG ARG A . n A 1 153 GLY 153 153 153 GLY GLY A . n A 1 154 LEU 154 154 154 LEU LEU A . n A 1 155 LYS 155 155 155 LYS LYS A . n A 1 156 VAL 156 156 156 VAL VAL A . n A 1 157 GLU 157 157 157 GLU GLU A . n A 1 158 ARG 158 158 158 ARG ARG A . n A 1 159 MSE 159 159 159 MSE MSE A . n A 1 160 SER 160 160 160 SER SER A . n A 1 161 LYS 161 161 161 LYS LYS A . n A 1 162 THR 162 162 162 THR THR A . n A 1 163 VAL 163 163 163 VAL VAL A . n A 1 164 TYR 164 164 164 TYR TYR A . n A 1 165 THR 165 165 165 THR THR A . n A 1 166 VAL 166 166 166 VAL VAL A . n A 1 167 ASP 167 167 167 ASP ASP A . n A 1 168 TRP 168 168 168 TRP TRP A . n A 1 169 VAL 169 169 169 VAL VAL A . n A 1 170 PRO 170 170 170 PRO PRO A . n A 1 171 PRO 171 171 171 PRO PRO A . n A 1 172 GLU 172 172 172 GLU GLU A . n A 1 173 CYS 173 173 173 CYS CYS A . n A 1 174 ILE 174 174 174 ILE ILE A . n A 1 175 ALA 175 175 175 ALA ALA A . n A 1 176 GLU 176 176 176 GLU GLU A . n A 1 177 VAL 177 177 177 VAL VAL A . n A 1 178 ARG 178 178 178 ARG ARG A . n A 1 179 ARG 179 179 179 ARG ARG A . n A 1 180 GLU 180 180 180 GLU GLU A . n A 1 181 SER 181 181 181 SER SER A . n A 1 182 LEU 182 182 182 LEU LEU A . n A 1 183 GLY 183 183 ? ? ? A . n A 1 184 ARG 184 184 ? ? ? A . n A 1 185 SER 185 185 ? ? ? A . n A 1 186 LEU 186 186 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # 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 ZN 1 201 201 ZN ZN A . C 3 CL 1 202 202 CL CL A . D 3 CL 1 203 203 CL CL A . E 3 CL 1 204 204 CL CL A . F 3 CL 1 205 205 CL CL A . G 3 CL 1 206 206 CL CL A . H 4 HOH 1 301 301 HOH HOH A . H 4 HOH 2 302 302 HOH HOH A . H 4 HOH 3 303 303 HOH HOH A . H 4 HOH 4 304 304 HOH HOH A . H 4 HOH 5 305 305 HOH HOH A . H 4 HOH 6 306 306 HOH HOH A . H 4 HOH 7 307 307 HOH HOH A . H 4 HOH 8 308 308 HOH HOH A . H 4 HOH 9 309 309 HOH HOH A . H 4 HOH 10 310 310 HOH HOH A . H 4 HOH 11 311 311 HOH HOH A . H 4 HOH 12 312 312 HOH HOH A . H 4 HOH 13 313 313 HOH HOH A . H 4 HOH 14 314 314 HOH HOH A . H 4 HOH 15 315 315 HOH HOH A . H 4 HOH 16 316 316 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 107 A MSE 107 ? MET SELENOMETHIONINE 2 A MSE 112 A MSE 112 ? MET SELENOMETHIONINE 3 A MSE 159 A MSE 159 ? MET SELENOMETHIONINE # 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_defined_assembly ? monomeric 1 2 software_defined_assembly PISA,PQS 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,D,E,F,G,H 2 1,2,3 A,B,C,D,E,F,G,H # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 2 'ABSA (A^2)' 5220 ? 2 MORE -186 ? 2 'SSA (A^2)' 27020 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5000000000 -0.8660254038 0.0000000000 51.3335000000 0.8660254038 -0.5000000000 0.0000000000 88.9122301303 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5000000000 0.8660254038 0.0000000000 -51.3335000000 -0.8660254038 -0.5000000000 0.0000000000 88.9122301303 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A ZN 201 ? B ZN . 2 1 A HOH 316 ? H HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? H HOH . ? A HOH 316 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 1_555 114.8 ? 2 O ? H HOH . ? A HOH 316 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 O ? H HOH . ? A HOH 316 ? 2_665 1.3 ? 3 NE2 ? A HIS 58 ? A HIS 58 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 O ? H HOH . ? A HOH 316 ? 2_665 116.1 ? 4 O ? H HOH . ? A HOH 316 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 O ? H HOH . ? A HOH 316 ? 3_565 1.3 ? 5 NE2 ? A HIS 58 ? A HIS 58 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 O ? H HOH . ? A HOH 316 ? 3_565 115.0 ? 6 O ? H HOH . ? A HOH 316 ? 2_665 ZN ? B ZN . ? A ZN 201 ? 1_555 O ? H HOH . ? A HOH 316 ? 3_565 1.3 ? 7 O ? H HOH . ? A HOH 316 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 2_665 113.8 ? 8 NE2 ? A HIS 58 ? A HIS 58 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 2_665 104.3 ? 9 O ? H HOH . ? A HOH 316 ? 2_665 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 2_665 113.6 ? 10 O ? H HOH . ? A HOH 316 ? 3_565 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 2_665 114.8 ? 11 O ? H HOH . ? A HOH 316 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 3_565 114.9 ? 12 NE2 ? A HIS 58 ? A HIS 58 ? 1_555 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 3_565 104.3 ? 13 O ? H HOH . ? A HOH 316 ? 2_665 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 3_565 113.9 ? 14 O ? H HOH . ? A HOH 316 ? 3_565 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 3_565 113.7 ? 15 NE2 ? A HIS 58 ? A HIS 58 ? 2_665 ZN ? B ZN . ? A ZN 201 ? 1_555 NE2 ? A HIS 58 ? A HIS 58 ? 3_565 103.4 ? # 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 2004-11-27 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Derived calculations' 3 3 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 HKL-2000 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 SOLVE phasing . ? 4 # 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 HIS A 15 ? ? -133.09 -33.78 2 1 ARG A 67 ? ? -174.07 142.47 3 1 ASN A 68 ? ? 7.08 74.06 4 1 THR A 98 ? ? -175.87 -166.26 5 1 LEU A 138 ? ? 77.24 60.04 # 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 MSE 1 ? A MSE 1 2 1 Y 1 A ARG 2 ? A ARG 2 3 1 Y 1 A GLY 183 ? A GLY 183 4 1 Y 1 A ARG 184 ? A ARG 184 5 1 Y 1 A SER 185 ? A SER 185 6 1 Y 1 A LEU 186 ? A LEU 186 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ZINC ION' ZN 3 'CHLORIDE ION' CL 4 water HOH #