data_3AKE # _entry.id 3AKE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.331 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3AKE RCSB RCSB029360 WWPDB D_1000029360 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2020-07-29 _pdbx_database_PDB_obs_spr.pdb_id 7CKJ _pdbx_database_PDB_obs_spr.replace_pdb_id 3AKE _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3AKC . unspecified PDB 3AKD . unspecified # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 3AKE _pdbx_database_status.recvd_initial_deposition_date 2010-07-12 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mega, R.' 1 'Nakagawa, N.' 2 'Kuramitsu, S.' 3 'Masui, R.' 4 # _citation.id primary _citation.title ;The crystal structure of the tertiary complex of CMP kinase with a phosphoryl group acceptor and a donor from Thermus thermophilus HB8 ; _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mega, R.' 1 ? primary 'Nakagawa, N.' 2 ? primary 'Kuramitsu, S.' 3 ? primary 'Masui, R.' 4 ? # _cell.entry_id 3AKE _cell.length_a 61.746 _cell.length_b 61.746 _cell.length_c 111.332 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3AKE _symmetry.space_group_name_H-M 'P 65' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _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 'Cytidylate kinase' 22584.818 1 2.7.4.14 ? ? ? 2 non-polymer syn "CYTIDINE-5'-MONOPHOSPHATE" 323.197 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 134 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'CK, Cytidine monophosphate kinase, CMP kinase' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;MRGIVTIDGPSASGKSSVARRVAAALGVPYLSSGLLYRAAAFLALRAGVDPGDEEGLLALLEGLGVRLLAQAEGNRVLAD GEDLTSFLHTPEVDRVVSAVARLPGVRAWVNRRLKEVPPPFVAEGRDMGTAVFPEAAHKFYLTASPEVRAWRRARERPQA YEEVLRDLLRRDERDKAQSAPAPDALVLDTGGMTLDEVVAWVLAHIRR ; _entity_poly.pdbx_seq_one_letter_code_can ;MRGIVTIDGPSASGKSSVARRVAAALGVPYLSSGLLYRAAAFLALRAGVDPGDEEGLLALLEGLGVRLLAQAEGNRVLAD GEDLTSFLHTPEVDRVVSAVARLPGVRAWVNRRLKEVPPPFVAEGRDMGTAVFPEAAHKFYLTASPEVRAWRRARERPQA YEEVLRDLLRRDERDKAQSAPAPDALVLDTGGMTLDEVVAWVLAHIRR ; _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 MET n 1 2 ARG n 1 3 GLY n 1 4 ILE n 1 5 VAL n 1 6 THR n 1 7 ILE n 1 8 ASP n 1 9 GLY n 1 10 PRO n 1 11 SER n 1 12 ALA n 1 13 SER n 1 14 GLY n 1 15 LYS n 1 16 SER n 1 17 SER n 1 18 VAL n 1 19 ALA n 1 20 ARG n 1 21 ARG n 1 22 VAL n 1 23 ALA n 1 24 ALA n 1 25 ALA n 1 26 LEU n 1 27 GLY n 1 28 VAL n 1 29 PRO n 1 30 TYR n 1 31 LEU n 1 32 SER n 1 33 SER n 1 34 GLY n 1 35 LEU n 1 36 LEU n 1 37 TYR n 1 38 ARG n 1 39 ALA n 1 40 ALA n 1 41 ALA n 1 42 PHE n 1 43 LEU n 1 44 ALA n 1 45 LEU n 1 46 ARG n 1 47 ALA n 1 48 GLY n 1 49 VAL n 1 50 ASP n 1 51 PRO n 1 52 GLY n 1 53 ASP n 1 54 GLU n 1 55 GLU n 1 56 GLY n 1 57 LEU n 1 58 LEU n 1 59 ALA n 1 60 LEU n 1 61 LEU n 1 62 GLU n 1 63 GLY n 1 64 LEU n 1 65 GLY n 1 66 VAL n 1 67 ARG n 1 68 LEU n 1 69 LEU n 1 70 ALA n 1 71 GLN n 1 72 ALA n 1 73 GLU n 1 74 GLY n 1 75 ASN n 1 76 ARG n 1 77 VAL n 1 78 LEU n 1 79 ALA n 1 80 ASP n 1 81 GLY n 1 82 GLU n 1 83 ASP n 1 84 LEU n 1 85 THR n 1 86 SER n 1 87 PHE n 1 88 LEU n 1 89 HIS n 1 90 THR n 1 91 PRO n 1 92 GLU n 1 93 VAL n 1 94 ASP n 1 95 ARG n 1 96 VAL n 1 97 VAL n 1 98 SER n 1 99 ALA n 1 100 VAL n 1 101 ALA n 1 102 ARG n 1 103 LEU n 1 104 PRO n 1 105 GLY n 1 106 VAL n 1 107 ARG n 1 108 ALA n 1 109 TRP n 1 110 VAL n 1 111 ASN n 1 112 ARG n 1 113 ARG n 1 114 LEU n 1 115 LYS n 1 116 GLU n 1 117 VAL n 1 118 PRO n 1 119 PRO n 1 120 PRO n 1 121 PHE n 1 122 VAL n 1 123 ALA n 1 124 GLU n 1 125 GLY n 1 126 ARG n 1 127 ASP n 1 128 MET n 1 129 GLY n 1 130 THR n 1 131 ALA n 1 132 VAL n 1 133 PHE n 1 134 PRO n 1 135 GLU n 1 136 ALA n 1 137 ALA n 1 138 HIS n 1 139 LYS n 1 140 PHE n 1 141 TYR n 1 142 LEU n 1 143 THR n 1 144 ALA n 1 145 SER n 1 146 PRO n 1 147 GLU n 1 148 VAL n 1 149 ARG n 1 150 ALA n 1 151 TRP n 1 152 ARG n 1 153 ARG n 1 154 ALA n 1 155 ARG n 1 156 GLU n 1 157 ARG n 1 158 PRO n 1 159 GLN n 1 160 ALA n 1 161 TYR n 1 162 GLU n 1 163 GLU n 1 164 VAL n 1 165 LEU n 1 166 ARG n 1 167 ASP n 1 168 LEU n 1 169 LEU n 1 170 ARG n 1 171 ARG n 1 172 ASP n 1 173 GLU n 1 174 ARG n 1 175 ASP n 1 176 LYS n 1 177 ALA n 1 178 GLN n 1 179 SER n 1 180 ALA n 1 181 PRO n 1 182 ALA n 1 183 PRO n 1 184 ASP n 1 185 ALA n 1 186 LEU n 1 187 VAL n 1 188 LEU n 1 189 ASP n 1 190 THR n 1 191 GLY n 1 192 GLY n 1 193 MET n 1 194 THR n 1 195 LEU n 1 196 ASP n 1 197 GLU n 1 198 VAL n 1 199 VAL n 1 200 ALA n 1 201 TRP n 1 202 VAL n 1 203 LEU n 1 204 ALA n 1 205 HIS n 1 206 ILE n 1 207 ARG n 1 208 ARG 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 TTHA0458 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain HB8 _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 'Thermus thermophilus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 300852 _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)' _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 pET-11a _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code KCY_THET8 _struct_ref.pdbx_db_accession Q5SL35 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MRGIVTIDGPSASGKSSVARRVAAALGVPYLSSGLLYRAAAFLALRAGVDPGDEEGLLALLEGLGVRLLAQAEGNRVLAD GEDLTSFLHTPEVDRVVSAVARLPGVRAWVNRRLKEVPPPFVAEGRDMGTAVFPEAAHKFYLTASPEVRAWRRARERPQA YEEVLRDLLRRDERDKAQSAPAPDALVLDTGGMTLDEVVAWVLAHIRR ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3AKE _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 208 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q5SL35 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 208 _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 208 # 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 C5P non-polymer . "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 3AKE _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.71 _exptl_crystal.density_percent_sol 54.66 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details '0.1M BIS-TRIS, 3.5M Sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 90 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2006-07-19 _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 'transparent diamond double crystal' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL45XU' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL45XU _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00000 # _reflns.entry_id 3AKE _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.50 _reflns.number_obs 38410 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.066 _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate 16.5 _reflns.pdbx_redundancy 8.1 _reflns.pdbx_netI_over_sigmaI 45.7 _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 1.50 _reflns_shell.d_res_low 1.55 _reflns_shell.percent_possible_all 99.8 _reflns_shell.Rmerge_I_obs 0.343 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 9.2 _reflns_shell.pdbx_redundancy 7.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 3801 _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 3AKE _refine.ls_number_reflns_obs 34495 _refine.ls_number_reflns_all 38329 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 1548291.40 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 38.56 _refine.ls_d_res_high 1.50 _refine.ls_percent_reflns_obs 99.7 _refine.ls_R_factor_obs 0.217 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.217 _refine.ls_R_factor_R_free 0.241 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 3834 _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 19.6 _refine.aniso_B[1][1] 3.03 _refine.aniso_B[2][2] 3.03 _refine.aniso_B[3][3] -6.07 _refine.aniso_B[1][2] 0.00 _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 0.45 _refine.solvent_model_param_bsol 55.724 _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 'BULK SOLVENT MODEL USED' _refine.pdbx_starting_model 'PDB ENTRY 2CMK' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_phase_error ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3AKE _refine_analyze.Luzzati_coordinate_error_obs 0.18 _refine_analyze.Luzzati_sigma_a_obs 0.08 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.21 _refine_analyze.Luzzati_sigma_a_free 0.09 _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 1577 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 22 _refine_hist.number_atoms_solvent 134 _refine_hist.number_atoms_total 1733 _refine_hist.d_res_high 1.50 _refine_hist.d_res_low 38.56 # 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 0.017 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 22.7 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.32 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.50 _refine_ls_shell.d_res_low 1.59 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.233 _refine_ls_shell.percent_reflns_obs 99.6 _refine_ls_shell.R_factor_R_free 0.265 _refine_ls_shell.R_factor_R_free_error 0.010 _refine_ls_shell.percent_reflns_R_free 10.5 _refine_ls_shell.number_reflns_R_free 667 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 5677 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 protein_rep.param protein.top 'X-RAY DIFFRACTION' 2 CMP.param CMP.top 'X-RAY DIFFRACTION' 4 water.param water.top 'X-RAY DIFFRACTION' 5 Mg2+.param Mg2+.top # _struct.entry_id 3AKE _struct.title 'Crystal structure of CMP kinase in complex with CMP from Thermus thermophilus HB8' _struct.pdbx_descriptor 'Cytidylate kinase (E.C.2.7.4.14)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3AKE _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text 'CMP kinase, CMP complex, open conformation, nucleotide metabolism, 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 4 ? # _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 GLY A 14 ? GLY A 27 ? GLY A 14 GLY A 27 1 ? 14 HELX_P HELX_P2 2 SER A 33 ? GLY A 48 ? SER A 33 GLY A 48 1 ? 16 HELX_P HELX_P3 3 ASP A 53 ? LEU A 64 ? ASP A 53 LEU A 64 1 ? 12 HELX_P HELX_P4 4 THR A 85 ? LEU A 88 ? THR A 85 LEU A 88 5 ? 4 HELX_P HELX_P5 5 THR A 90 ? ARG A 102 ? THR A 90 ARG A 102 1 ? 13 HELX_P HELX_P6 6 LEU A 103 ? VAL A 117 ? LEU A 103 VAL A 117 1 ? 15 HELX_P HELX_P7 7 SER A 145 ? GLU A 156 ? SER A 145 GLU A 156 1 ? 12 HELX_P HELX_P8 8 ALA A 160 ? ARG A 174 ? ALA A 160 ARG A 174 1 ? 15 HELX_P HELX_P9 9 THR A 194 ? ARG A 208 ? THR A 194 ARG A 208 1 ? 15 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id PRO _struct_mon_prot_cis.label_seq_id 119 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id PRO _struct_mon_prot_cis.auth_seq_id 119 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 120 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 120 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 0.03 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 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 ? parallel A 2 3 ? parallel A 3 4 ? parallel A 4 5 ? parallel B 1 2 ? anti-parallel B 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 TYR A 30 ? SER A 32 ? TYR A 30 SER A 32 A 2 PHE A 121 ? GLY A 125 ? PHE A 121 GLY A 125 A 3 ILE A 4 ? ASP A 8 ? ILE A 4 ASP A 8 A 4 HIS A 138 ? THR A 143 ? HIS A 138 THR A 143 A 5 LEU A 186 ? ASP A 189 ? LEU A 186 ASP A 189 B 1 ARG A 67 ? LEU A 69 ? ARG A 67 LEU A 69 B 2 ARG A 76 ? ALA A 79 ? ARG A 76 ALA A 79 B 3 GLU A 82 ? ASP A 83 ? GLU A 82 ASP A 83 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N LEU A 31 ? N LEU A 31 O GLU A 124 ? O GLU A 124 A 2 3 O ALA A 123 ? O ALA A 123 N VAL A 5 ? N VAL A 5 A 3 4 N ASP A 8 ? N ASP A 8 O LEU A 142 ? O LEU A 142 A 4 5 N TYR A 141 ? N TYR A 141 O LEU A 186 ? O LEU A 186 B 1 2 N LEU A 69 ? N LEU A 69 O ARG A 76 ? O ARG A 76 B 2 3 N ALA A 79 ? N ALA A 79 O GLU A 82 ? O GLU A 82 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A C5P 209 ? 16 'BINDING SITE FOR RESIDUE C5P A 209' AC2 Software A MG 210 ? 3 'BINDING SITE FOR RESIDUE MG A 210' # 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 16 SER A 11 ? SER A 11 . ? 1_555 ? 2 AC1 16 LYS A 15 ? LYS A 15 . ? 1_555 ? 3 AC1 16 SER A 33 ? SER A 33 . ? 1_555 ? 4 AC1 16 GLY A 34 ? GLY A 34 . ? 1_555 ? 5 AC1 16 TYR A 37 ? TYR A 37 . ? 1_555 ? 6 AC1 16 ARG A 38 ? ARG A 38 . ? 1_555 ? 7 AC1 16 VAL A 97 ? VAL A 97 . ? 1_555 ? 8 AC1 16 ALA A 101 ? ALA A 101 . ? 1_555 ? 9 AC1 16 ARG A 107 ? ARG A 107 . ? 1_555 ? 10 AC1 16 GLY A 125 ? GLY A 125 . ? 1_555 ? 11 AC1 16 ARG A 126 ? ARG A 126 . ? 1_555 ? 12 AC1 16 ASP A 127 ? ASP A 127 . ? 1_555 ? 13 AC1 16 MET A 128 ? MET A 128 . ? 1_555 ? 14 AC1 16 HOH D . ? HOH A 229 . ? 1_555 ? 15 AC1 16 HOH D . ? HOH A 230 . ? 1_555 ? 16 AC1 16 HOH D . ? HOH A 254 . ? 1_555 ? 17 AC2 3 GLY A 14 ? GLY A 14 . ? 1_555 ? 18 AC2 3 LYS A 15 ? LYS A 15 . ? 1_555 ? 19 AC2 3 SER A 16 ? SER A 16 . ? 1_555 ? # _database_PDB_matrix.entry_id 3AKE _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 3AKE _atom_sites.fract_transf_matrix[1][1] 0.016195 _atom_sites.fract_transf_matrix[1][2] 0.009350 _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] 0.018701 _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] 0.008982 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P S # loop_ # 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 MET 1 1 1 MET MET A . n A 1 2 ARG 2 2 2 ARG ARG A . n A 1 3 GLY 3 3 3 GLY GLY A . n A 1 4 ILE 4 4 4 ILE ILE A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 THR 6 6 6 THR THR A . n A 1 7 ILE 7 7 7 ILE ILE A . n A 1 8 ASP 8 8 8 ASP ASP A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 PRO 10 10 10 PRO PRO A . n A 1 11 SER 11 11 11 SER SER A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 SER 13 13 13 SER SER A . n A 1 14 GLY 14 14 14 GLY GLY A . n A 1 15 LYS 15 15 15 LYS LYS A . n A 1 16 SER 16 16 16 SER SER A . n A 1 17 SER 17 17 17 SER SER A . n A 1 18 VAL 18 18 18 VAL VAL A . n A 1 19 ALA 19 19 19 ALA ALA A . n A 1 20 ARG 20 20 20 ARG ARG A . n A 1 21 ARG 21 21 21 ARG ARG A . n A 1 22 VAL 22 22 22 VAL VAL A . n A 1 23 ALA 23 23 23 ALA ALA A . n A 1 24 ALA 24 24 24 ALA ALA A . n A 1 25 ALA 25 25 25 ALA ALA A . n A 1 26 LEU 26 26 26 LEU LEU A . n A 1 27 GLY 27 27 27 GLY GLY A . n A 1 28 VAL 28 28 28 VAL VAL A . n A 1 29 PRO 29 29 29 PRO PRO A . n A 1 30 TYR 30 30 30 TYR TYR A . n A 1 31 LEU 31 31 31 LEU LEU A . n A 1 32 SER 32 32 32 SER SER A . n A 1 33 SER 33 33 33 SER SER A . n A 1 34 GLY 34 34 34 GLY GLY A . n A 1 35 LEU 35 35 35 LEU LEU A . n A 1 36 LEU 36 36 36 LEU LEU A . n A 1 37 TYR 37 37 37 TYR TYR A . n A 1 38 ARG 38 38 38 ARG ARG A . n A 1 39 ALA 39 39 39 ALA ALA A . n A 1 40 ALA 40 40 40 ALA ALA A . n A 1 41 ALA 41 41 41 ALA ALA A . n A 1 42 PHE 42 42 42 PHE PHE A . n A 1 43 LEU 43 43 43 LEU LEU A . n A 1 44 ALA 44 44 44 ALA ALA A . n A 1 45 LEU 45 45 45 LEU LEU A . n A 1 46 ARG 46 46 46 ARG ARG A . n A 1 47 ALA 47 47 47 ALA ALA A . n A 1 48 GLY 48 48 48 GLY GLY A . n A 1 49 VAL 49 49 49 VAL VAL A . n A 1 50 ASP 50 50 50 ASP ASP A . n A 1 51 PRO 51 51 51 PRO PRO A . n A 1 52 GLY 52 52 52 GLY GLY A . n A 1 53 ASP 53 53 53 ASP ASP A . n A 1 54 GLU 54 54 54 GLU GLU A . n A 1 55 GLU 55 55 55 GLU GLU A . n A 1 56 GLY 56 56 56 GLY GLY A . n A 1 57 LEU 57 57 57 LEU LEU A . n A 1 58 LEU 58 58 58 LEU LEU A . n A 1 59 ALA 59 59 59 ALA ALA A . n A 1 60 LEU 60 60 60 LEU LEU A . n A 1 61 LEU 61 61 61 LEU LEU A . n A 1 62 GLU 62 62 62 GLU GLU A . n A 1 63 GLY 63 63 63 GLY GLY A . n A 1 64 LEU 64 64 64 LEU LEU A . n A 1 65 GLY 65 65 65 GLY GLY A . n A 1 66 VAL 66 66 66 VAL VAL A . n A 1 67 ARG 67 67 67 ARG ARG A . n A 1 68 LEU 68 68 68 LEU LEU A . n A 1 69 LEU 69 69 69 LEU LEU A . n A 1 70 ALA 70 70 70 ALA ALA A . n A 1 71 GLN 71 71 71 GLN GLN A . n A 1 72 ALA 72 72 72 ALA ALA A . n A 1 73 GLU 73 73 73 GLU GLU A . n A 1 74 GLY 74 74 74 GLY GLY A . n A 1 75 ASN 75 75 75 ASN ASN A . n A 1 76 ARG 76 76 76 ARG ARG A . n A 1 77 VAL 77 77 77 VAL VAL A . n A 1 78 LEU 78 78 78 LEU LEU A . n A 1 79 ALA 79 79 79 ALA ALA A . n A 1 80 ASP 80 80 80 ASP ASP A . n A 1 81 GLY 81 81 81 GLY GLY A . n A 1 82 GLU 82 82 82 GLU GLU A . n A 1 83 ASP 83 83 83 ASP ASP A . n A 1 84 LEU 84 84 84 LEU LEU A . n A 1 85 THR 85 85 85 THR THR A . n A 1 86 SER 86 86 86 SER SER A . n A 1 87 PHE 87 87 87 PHE PHE A . n A 1 88 LEU 88 88 88 LEU LEU A . n A 1 89 HIS 89 89 89 HIS HIS A . n A 1 90 THR 90 90 90 THR THR A . n A 1 91 PRO 91 91 91 PRO PRO A . n A 1 92 GLU 92 92 92 GLU GLU A . n A 1 93 VAL 93 93 93 VAL VAL A . n A 1 94 ASP 94 94 94 ASP ASP A . n A 1 95 ARG 95 95 95 ARG ARG A . n A 1 96 VAL 96 96 96 VAL VAL A . n A 1 97 VAL 97 97 97 VAL VAL A . n A 1 98 SER 98 98 98 SER SER A . n A 1 99 ALA 99 99 99 ALA ALA A . n A 1 100 VAL 100 100 100 VAL VAL A . n A 1 101 ALA 101 101 101 ALA ALA A . n A 1 102 ARG 102 102 102 ARG ARG 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 GLY 105 105 105 GLY GLY A . n A 1 106 VAL 106 106 106 VAL VAL A . n A 1 107 ARG 107 107 107 ARG ARG A . n A 1 108 ALA 108 108 108 ALA ALA A . n A 1 109 TRP 109 109 109 TRP TRP A . n A 1 110 VAL 110 110 110 VAL VAL A . n A 1 111 ASN 111 111 111 ASN ASN A . n A 1 112 ARG 112 112 112 ARG ARG A . n A 1 113 ARG 113 113 113 ARG ARG A . n A 1 114 LEU 114 114 114 LEU LEU A . n A 1 115 LYS 115 115 115 LYS LYS A . n A 1 116 GLU 116 116 116 GLU GLU A . n A 1 117 VAL 117 117 117 VAL VAL A . n A 1 118 PRO 118 118 118 PRO PRO A . n A 1 119 PRO 119 119 119 PRO PRO A . n A 1 120 PRO 120 120 120 PRO PRO A . n A 1 121 PHE 121 121 121 PHE PHE A . n A 1 122 VAL 122 122 122 VAL VAL A . n A 1 123 ALA 123 123 123 ALA ALA A . n A 1 124 GLU 124 124 124 GLU GLU A . n A 1 125 GLY 125 125 125 GLY GLY A . n A 1 126 ARG 126 126 126 ARG ARG A . n A 1 127 ASP 127 127 127 ASP ASP A . n A 1 128 MET 128 128 128 MET MET A . n A 1 129 GLY 129 129 129 GLY GLY A . n A 1 130 THR 130 130 130 THR THR A . n A 1 131 ALA 131 131 131 ALA ALA A . n A 1 132 VAL 132 132 132 VAL VAL A . n A 1 133 PHE 133 133 133 PHE PHE A . n A 1 134 PRO 134 134 134 PRO PRO A . n A 1 135 GLU 135 135 135 GLU GLU A . n A 1 136 ALA 136 136 136 ALA ALA A . n A 1 137 ALA 137 137 137 ALA ALA A . n A 1 138 HIS 138 138 138 HIS HIS A . n A 1 139 LYS 139 139 139 LYS LYS A . n A 1 140 PHE 140 140 140 PHE PHE A . n A 1 141 TYR 141 141 141 TYR TYR A . n A 1 142 LEU 142 142 142 LEU LEU A . n A 1 143 THR 143 143 143 THR THR A . n A 1 144 ALA 144 144 144 ALA ALA A . n A 1 145 SER 145 145 145 SER SER A . n A 1 146 PRO 146 146 146 PRO PRO A . n A 1 147 GLU 147 147 147 GLU GLU A . n A 1 148 VAL 148 148 148 VAL VAL A . n A 1 149 ARG 149 149 149 ARG ARG A . n A 1 150 ALA 150 150 150 ALA ALA A . n A 1 151 TRP 151 151 151 TRP TRP A . n A 1 152 ARG 152 152 152 ARG ARG A . n A 1 153 ARG 153 153 153 ARG ARG A . n A 1 154 ALA 154 154 154 ALA ALA A . n A 1 155 ARG 155 155 155 ARG ARG A . n A 1 156 GLU 156 156 156 GLU GLU A . n A 1 157 ARG 157 157 157 ARG ARG A . n A 1 158 PRO 158 158 158 PRO PRO A . n A 1 159 GLN 159 159 159 GLN GLN A . n A 1 160 ALA 160 160 160 ALA ALA A . n A 1 161 TYR 161 161 161 TYR TYR A . n A 1 162 GLU 162 162 162 GLU GLU A . n A 1 163 GLU 163 163 163 GLU GLU A . n A 1 164 VAL 164 164 164 VAL VAL A . n A 1 165 LEU 165 165 165 LEU LEU A . n A 1 166 ARG 166 166 166 ARG ARG A . n A 1 167 ASP 167 167 167 ASP ASP A . n A 1 168 LEU 168 168 168 LEU LEU A . n A 1 169 LEU 169 169 169 LEU LEU A . n A 1 170 ARG 170 170 170 ARG ARG A . n A 1 171 ARG 171 171 171 ARG ARG A . n A 1 172 ASP 172 172 172 ASP ASP A . n A 1 173 GLU 173 173 173 GLU GLU A . n A 1 174 ARG 174 174 174 ARG ARG A . n A 1 175 ASP 175 175 175 ASP ASP A . n A 1 176 LYS 176 176 ? ? ? A . n A 1 177 ALA 177 177 ? ? ? A . n A 1 178 GLN 178 178 178 GLN GLN A . n A 1 179 SER 179 179 179 SER SER A . n A 1 180 ALA 180 180 180 ALA ALA A . n A 1 181 PRO 181 181 181 PRO PRO A . n A 1 182 ALA 182 182 182 ALA ALA A . n A 1 183 PRO 183 183 183 PRO PRO A . n A 1 184 ASP 184 184 184 ASP ASP A . n A 1 185 ALA 185 185 185 ALA ALA A . n A 1 186 LEU 186 186 186 LEU LEU A . n A 1 187 VAL 187 187 187 VAL VAL A . n A 1 188 LEU 188 188 188 LEU LEU A . n A 1 189 ASP 189 189 189 ASP ASP A . n A 1 190 THR 190 190 190 THR THR A . n A 1 191 GLY 191 191 191 GLY GLY A . n A 1 192 GLY 192 192 192 GLY GLY A . n A 1 193 MET 193 193 193 MET MET A . n A 1 194 THR 194 194 194 THR THR A . n A 1 195 LEU 195 195 195 LEU LEU A . n A 1 196 ASP 196 196 196 ASP ASP A . n A 1 197 GLU 197 197 197 GLU GLU A . n A 1 198 VAL 198 198 198 VAL VAL A . n A 1 199 VAL 199 199 199 VAL VAL A . n A 1 200 ALA 200 200 200 ALA ALA A . n A 1 201 TRP 201 201 201 TRP TRP A . n A 1 202 VAL 202 202 202 VAL VAL A . n A 1 203 LEU 203 203 203 LEU LEU A . n A 1 204 ALA 204 204 204 ALA ALA A . n A 1 205 HIS 205 205 205 HIS HIS A . n A 1 206 ILE 206 206 206 ILE ILE A . n A 1 207 ARG 207 207 207 ARG ARG A . n A 1 208 ARG 208 208 208 ARG ARG 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 C5P 1 209 1 C5P C5P A . C 3 MG 1 210 75 MG MG A . D 4 HOH 1 211 1 HOH TIP A . D 4 HOH 2 212 2 HOH TIP A . D 4 HOH 3 213 3 HOH TIP A . D 4 HOH 4 214 5 HOH TIP A . D 4 HOH 5 215 8 HOH TIP A . D 4 HOH 6 216 9 HOH TIP A . D 4 HOH 7 217 10 HOH TIP A . D 4 HOH 8 218 11 HOH TIP A . D 4 HOH 9 219 12 HOH TIP A . D 4 HOH 10 220 13 HOH TIP A . D 4 HOH 11 221 14 HOH TIP A . D 4 HOH 12 222 15 HOH TIP A . D 4 HOH 13 223 16 HOH TIP A . D 4 HOH 14 224 17 HOH TIP A . D 4 HOH 15 225 18 HOH TIP A . D 4 HOH 16 226 19 HOH TIP A . D 4 HOH 17 227 20 HOH TIP A . D 4 HOH 18 228 21 HOH TIP A . D 4 HOH 19 229 22 HOH TIP A . D 4 HOH 20 230 23 HOH TIP A . D 4 HOH 21 231 24 HOH TIP A . D 4 HOH 22 232 25 HOH TIP A . D 4 HOH 23 233 26 HOH TIP A . D 4 HOH 24 234 27 HOH TIP A . D 4 HOH 25 235 28 HOH TIP A . D 4 HOH 26 236 29 HOH TIP A . D 4 HOH 27 237 30 HOH TIP A . D 4 HOH 28 238 31 HOH TIP A . D 4 HOH 29 239 32 HOH TIP A . D 4 HOH 30 240 33 HOH TIP A . D 4 HOH 31 241 34 HOH TIP A . D 4 HOH 32 242 35 HOH TIP A . D 4 HOH 33 243 36 HOH TIP A . D 4 HOH 34 244 37 HOH TIP A . D 4 HOH 35 245 38 HOH TIP A . D 4 HOH 36 246 39 HOH TIP A . D 4 HOH 37 247 40 HOH TIP A . D 4 HOH 38 248 41 HOH TIP A . D 4 HOH 39 249 42 HOH TIP A . D 4 HOH 40 250 43 HOH TIP A . D 4 HOH 41 251 44 HOH TIP A . D 4 HOH 42 252 45 HOH TIP A . D 4 HOH 43 253 46 HOH TIP A . D 4 HOH 44 254 47 HOH TIP A . D 4 HOH 45 255 48 HOH TIP A . D 4 HOH 46 256 49 HOH TIP A . D 4 HOH 47 257 50 HOH TIP A . D 4 HOH 48 258 51 HOH TIP A . D 4 HOH 49 259 52 HOH TIP A . D 4 HOH 50 260 53 HOH TIP A . D 4 HOH 51 261 54 HOH TIP A . D 4 HOH 52 262 55 HOH TIP A . D 4 HOH 53 263 56 HOH TIP A . D 4 HOH 54 264 57 HOH TIP A . D 4 HOH 55 265 58 HOH TIP A . D 4 HOH 56 266 59 HOH TIP A . D 4 HOH 57 267 60 HOH TIP A . D 4 HOH 58 268 61 HOH TIP A . D 4 HOH 59 269 62 HOH TIP A . D 4 HOH 60 270 63 HOH TIP A . D 4 HOH 61 271 64 HOH TIP A . D 4 HOH 62 272 65 HOH TIP A . D 4 HOH 63 273 66 HOH TIP A . D 4 HOH 64 274 67 HOH TIP A . D 4 HOH 65 275 68 HOH TIP A . D 4 HOH 66 276 70 HOH TIP A . D 4 HOH 67 277 71 HOH TIP A . D 4 HOH 68 278 72 HOH TIP A . D 4 HOH 69 279 73 HOH TIP A . D 4 HOH 70 280 74 HOH TIP A . D 4 HOH 71 281 75 HOH TIP A . D 4 HOH 72 282 76 HOH TIP A . D 4 HOH 73 283 77 HOH TIP A . D 4 HOH 74 284 78 HOH TIP A . D 4 HOH 75 285 79 HOH TIP A . D 4 HOH 76 286 80 HOH TIP A . D 4 HOH 77 287 81 HOH TIP A . D 4 HOH 78 288 83 HOH TIP A . D 4 HOH 79 289 84 HOH TIP A . D 4 HOH 80 290 85 HOH TIP A . D 4 HOH 81 291 86 HOH TIP A . D 4 HOH 82 292 87 HOH TIP A . D 4 HOH 83 293 88 HOH TIP A . D 4 HOH 84 294 89 HOH TIP A . D 4 HOH 85 295 90 HOH TIP A . D 4 HOH 86 296 92 HOH TIP A . D 4 HOH 87 297 93 HOH TIP A . D 4 HOH 88 298 95 HOH TIP A . D 4 HOH 89 299 96 HOH TIP A . D 4 HOH 90 300 97 HOH TIP A . D 4 HOH 91 301 98 HOH TIP A . D 4 HOH 92 302 99 HOH TIP A . D 4 HOH 93 303 100 HOH TIP A . D 4 HOH 94 304 101 HOH TIP A . D 4 HOH 95 305 102 HOH TIP A . D 4 HOH 96 306 103 HOH TIP A . D 4 HOH 97 307 104 HOH TIP A . D 4 HOH 98 308 105 HOH TIP A . D 4 HOH 99 309 106 HOH TIP A . D 4 HOH 100 310 107 HOH TIP A . D 4 HOH 101 311 108 HOH TIP A . D 4 HOH 102 312 109 HOH TIP A . D 4 HOH 103 313 110 HOH TIP A . D 4 HOH 104 314 111 HOH TIP A . D 4 HOH 105 315 112 HOH TIP A . D 4 HOH 106 316 113 HOH TIP A . D 4 HOH 107 317 114 HOH TIP A . D 4 HOH 108 318 115 HOH TIP A . D 4 HOH 109 319 116 HOH TIP A . D 4 HOH 110 320 117 HOH TIP A . D 4 HOH 111 321 118 HOH TIP A . D 4 HOH 112 322 119 HOH TIP A . D 4 HOH 113 323 121 HOH TIP A . D 4 HOH 114 324 122 HOH TIP A . D 4 HOH 115 325 123 HOH TIP A . D 4 HOH 116 326 124 HOH TIP A . D 4 HOH 117 327 125 HOH TIP A . D 4 HOH 118 328 126 HOH TIP A . D 4 HOH 119 329 127 HOH TIP A . D 4 HOH 120 330 129 HOH TIP A . D 4 HOH 121 331 130 HOH TIP A . D 4 HOH 122 332 131 HOH TIP A . D 4 HOH 123 333 132 HOH TIP A . D 4 HOH 124 334 133 HOH TIP A . D 4 HOH 125 335 134 HOH TIP A . D 4 HOH 126 336 136 HOH TIP A . D 4 HOH 127 337 137 HOH TIP A . D 4 HOH 128 338 138 HOH TIP A . D 4 HOH 129 339 140 HOH TIP A . D 4 HOH 130 340 142 HOH TIP A . D 4 HOH 131 341 144 HOH TIP A . D 4 HOH 132 342 146 HOH TIP A . D 4 HOH 133 343 147 HOH TIP A . D 4 HOH 134 344 150 HOH TIP A . # _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 2011-07-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 3 'Structure model' repository Obsolete ? ? # 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' Advisory 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' Other # 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 3 'Structure model' pdbx_database_PDB_obs_spr 2 3 'Structure model' pdbx_database_status 3 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_pdbx_database_status.status_code' 2 3 'Structure model' '_pdbx_database_status.status_code_sf' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 ARP/wARP 'model building' 7.1 ? 2 CNS refinement 1.2 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id HIS _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 89 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -106.36 _pdbx_validate_torsion.psi 64.48 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A LYS 176 ? A LYS 176 2 1 Y 1 A ALA 177 ? A ALA 177 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "CYTIDINE-5'-MONOPHOSPHATE" C5P 3 'MAGNESIUM ION' MG 4 water HOH #