data_3W8N # _entry.id 3W8N # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3W8N RCSB RCSB096024 WWPDB D_1000096024 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3AKC 'The same protein complexed with CDP and ADP' unspecified PDB 3AKD 'The same protein complexed with CDP' unspecified PDB 3AKE 'The same protein complexed with CMP' unspecified TargetTrack RSGI-ttk003000091.2 . unspecified # _pdbx_database_status.entry_id 3W8N _pdbx_database_status.methods_development_category ? _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2013-03-19 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nakagawa, N.' 1 'Mega, R.' 2 'Masui, R.' 3 'Kuramitsu, S.' 4 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 5 # _citation.id primary _citation.title 'Crystal structure of CMP kinase: insights into initial substrate recognition and reaction mechanisms' _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 primary 'Mega, R.' 1 primary 'Nakagawa, N.' 2 primary 'Masui, R.' 3 primary 'Kuramitsu, S.' 4 # _cell.length_a 49.212 _cell.length_b 49.212 _cell.length_c 98.051 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3W8N _cell.pdbx_unique_axis ? _cell.Z_PDB 3 _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.space_group_name_H-M 'P 31' _symmetry.entry_id 3W8N _symmetry.Int_Tables_number 144 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Cytidylate kinase' 22725.502 1 2.7.4.25 ? ? ? 2 non-polymer syn "CYTIDINE-5'-MONOPHOSPHATE" 323.197 1 ? ? ? ? 3 water nat water 18.015 84 ? ? ? ? # _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 yes _entity_poly.pdbx_seq_one_letter_code ;(MSE)RGIVTIDGPSASGKSSVARRVAAALGVPYLSSGLLYRAAAFLALRAGVDPGDEEGLLALLEGLGVRLLAQAEGNR VLADGEDLTSFLHTPEVDRVVSAVARLPGVRAWVNRRLKEVPPPFVAEGRD(MSE)GTAVFPEAAHKFYLTASPEVRAWR RARERPQAYEEVLRDLLRRDERDKAQSAPAPDALVLDTGG(MSE)TLDEVVAWVLAHIRR ; _entity_poly.pdbx_seq_one_letter_code_can ;MRGIVTIDGPSASGKSSVARRVAAALGVPYLSSGLLYRAAAFLALRAGVDPGDEEGLLALLEGLGVRLLAQAEGNRVLAD GEDLTSFLHTPEVDRVVSAVARLPGVRAWVNRRLKEVPPPFVAEGRDMGTAVFPEAAHKFYLTASPEVRAWRRARERPQA YEEVLRDLLRRDERDKAQSAPAPDALVLDTGGMTLDEVVAWVLAHIRR ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier RSGI-ttk003000091.2 # 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 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 MSE 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 MSE 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 'B834(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 3W8N _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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 3W8N _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity 0.354 _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 3.02 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 59.22 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details '10mM CMP, 10mM MgCl2, 0.6M sodium succinate, pH 7.0, VAPOR DIFFUSION, HANGING 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 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS V' _diffrn_detector.pdbx_collection_date 2004-04-10 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'transparent double crystal' _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9791 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL45PX' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9791 _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL45PX # _reflns.entry_id 3W8N _reflns.d_resolution_high 2.200 _reflns.d_resolution_low 50.000 _reflns.number_obs 26811 _reflns.pdbx_Rmerge_I_obs 0.049 _reflns.pdbx_netI_over_sigmaI 23.300 _reflns.pdbx_chi_squared 1.767 _reflns.percent_possible_obs 99.500 _reflns.observed_criterion_sigma_F -3 _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 2.0 _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_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.200 2.280 ? ? ? ? 0.262 ? ? 1.298 ? ? ? ? 2684 ? ? ? ? 99.200 ? ? 1 1 2.280 2.370 ? ? ? ? 0.205 ? ? 1.379 ? ? ? ? 2646 ? ? ? ? 99.400 ? ? 2 1 2.370 2.480 ? ? ? ? 0.151 ? ? 1.533 ? ? ? ? 2692 ? ? ? ? 99.300 ? ? 3 1 2.480 2.610 ? ? ? ? 0.124 ? ? 1.749 ? ? ? ? 2671 ? ? ? ? 99.500 ? ? 4 1 2.610 2.770 ? ? ? ? 0.093 ? ? 1.763 ? ? ? ? 2696 ? ? ? ? 99.600 ? ? 5 1 2.770 2.990 ? ? ? ? 0.072 ? ? 1.938 ? ? ? ? 2644 ? ? ? ? 99.500 ? ? 6 1 2.990 3.290 ? ? ? ? 0.056 ? ? 2.145 ? ? ? ? 2725 ? ? ? ? 99.500 ? ? 7 1 3.290 3.760 ? ? ? ? 0.046 ? ? 2.249 ? ? ? ? 2669 ? ? ? ? 99.600 ? ? 8 1 3.760 4.740 ? ? ? ? 0.037 ? ? 1.880 ? ? ? ? 2682 ? ? ? ? 99.800 ? ? 9 1 4.740 50.000 ? ? ? ? 0.032 ? ? 1.717 ? ? ? ? 2702 ? ? ? ? 99.400 ? ? 10 1 # _refine.entry_id 3W8N _refine.ls_d_res_high 2.2000 _refine.ls_d_res_low 42.6200 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF 821362.0000 _refine.pdbx_data_cutoff_low_absF 0.0000 _refine.ls_percent_reflns_obs 96.5000 _refine.ls_number_reflns_obs 26009 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'BULK SOLVENT MODEL USED' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1990 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2450 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 9.5000 _refine.ls_number_reflns_R_free 2462 _refine.ls_R_factor_R_free_error 0.0050 _refine.B_iso_mean 37.6258 _refine.solvent_model_param_bsol 40.7231 _refine.solvent_model_param_ksol 0.4000 _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.aniso_B[1][1] -0.1700 _refine.aniso_B[2][2] -0.1700 _refine.aniso_B[3][3] 0.3400 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT MODEL' _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8396 _refine.B_iso_max 85.000 _refine.B_iso_min 18.160 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3W8N _refine_analyze.Luzzati_coordinate_error_obs 0.260 _refine_analyze.Luzzati_sigma_a_obs 0.240 _refine_analyze.Luzzati_d_res_low_obs 5.000 _refine_analyze.Luzzati_coordinate_error_free 0.330 _refine_analyze.Luzzati_sigma_a_free 0.300 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_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 1518 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 21 _refine_hist.number_atoms_solvent 84 _refine_hist.number_atoms_total 1623 _refine_hist.d_res_high 2.2000 _refine_hist.d_res_low 42.6200 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id c_bond_d ? 0.008 ? ? ? 'X-RAY DIFFRACTION' c_angle_deg ? 1.400 ? ? ? 'X-RAY DIFFRACTION' c_dihedral_angle_d ? 22.600 ? ? ? 'X-RAY DIFFRACTION' c_improper_angle_d ? 1.400 ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it ? 2.050 1.500 ? ? 'X-RAY DIFFRACTION' c_mcangle_it ? 3.020 2.000 ? ? 'X-RAY DIFFRACTION' c_scbond_it ? 3.810 2.000 ? ? 'X-RAY DIFFRACTION' c_scangle_it ? 5.060 2.500 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.2000 _refine_ls_shell.d_res_low 2.3400 _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.percent_reflns_obs 89.6000 _refine_ls_shell.number_reflns_R_work 3632 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2640 _refine_ls_shell.R_factor_R_free 0.3190 _refine_ls_shell.percent_reflns_R_free 10.2000 _refine_ls_shell.number_reflns_R_free 411 _refine_ls_shell.R_factor_R_free_error 0.0160 _refine_ls_shell.number_reflns_all 4043 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.redundancy_reflns_obs ? # 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.param protein.top 'X-RAY DIFFRACTION' 2 dna-rna.param dna-rna.top 'X-RAY DIFFRACTION' 3 water.param water.top 'X-RAY DIFFRACTION' 4 ion.param ion.top 'X-RAY DIFFRACTION' 5 carbohydrate.param carbohydrate.top 'X-RAY DIFFRACTION' 6 c5p.param c5p.top # _struct.entry_id 3W8N _struct.title 'Open form structure of CMP kinase in complex with CMP from Thermus thermophilus HB8' _struct.pdbx_descriptor 'Cytidylate kinase (E.C.2.7.4.25)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3W8N _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text ;Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, kinase, CMP, 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 ? # _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 ? GLY A 65 ? ASP A 53 GLY A 65 1 ? 13 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 ? GLU A 116 ? LEU A 103 GLU A 116 1 ? 14 HELX_P HELX_P7 7 SER A 145 ? ALA A 154 ? SER A 145 ALA A 154 1 ? 10 HELX_P HELX_P8 8 ALA A 160 ? ASP A 175 ? ALA A 160 ASP A 175 1 ? 16 HELX_P HELX_P9 9 LYS A 176 ? SER A 179 ? LYS A 176 SER A 179 5 ? 4 HELX_P HELX_P10 10 THR A 194 ? ALA A 204 ? THR A 194 ALA A 204 1 ? 11 # _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 ASP 127 C ? ? ? 1_555 A MSE 128 N ? ? A ASP 127 A MSE 128 1_555 ? ? ? ? ? ? ? 1.330 ? covale2 covale ? ? A MSE 128 C ? ? ? 1_555 A GLY 129 N ? ? A MSE 128 A GLY 129 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A GLY 192 C ? ? ? 1_555 A MSE 193 N ? ? A GLY 192 A MSE 193 1_555 ? ? ? ? ? ? ? 1.333 ? covale4 covale ? ? A MSE 193 C ? ? ? 1_555 A THR 194 N ? ? A MSE 193 A THR 194 1_555 ? ? ? ? ? ? ? 1.323 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_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 0.05 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 3 ? C ? 2 ? # 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 B 1 2 ? anti-parallel B 2 3 ? anti-parallel C 1 2 ? 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 PHE A 121 ? ALA A 123 ? PHE A 121 ALA A 123 A 2 ILE A 4 ? ASP A 8 ? ILE A 4 ASP A 8 A 3 HIS A 138 ? THR A 143 ? HIS A 138 THR A 143 A 4 LEU A 186 ? ASP A 189 ? LEU A 186 ASP A 189 B 1 VAL A 66 ? LEU A 69 ? VAL A 66 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 C 1 ARG A 126 ? ASP A 127 ? ARG A 126 ASP A 127 C 2 THR A 130 ? ALA A 131 ? THR A 130 ALA A 131 # 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 O PHE A 121 ? O PHE A 121 N VAL A 5 ? N VAL A 5 A 2 3 N ASP A 8 ? N ASP A 8 O LEU A 142 ? O LEU A 142 A 3 4 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 C 1 2 N ASP A 127 ? N ASP A 127 O THR A 130 ? O THR A 130 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'BINDING SITE FOR RESIDUE C5P A 301' # 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 9 GLY A 34 ? GLY A 34 . ? 1_555 ? 2 AC1 9 TYR A 37 ? TYR A 37 . ? 1_555 ? 3 AC1 9 ARG A 38 ? ARG A 38 . ? 1_555 ? 4 AC1 9 SER A 98 ? SER A 98 . ? 1_555 ? 5 AC1 9 ALA A 101 ? ALA A 101 . ? 1_555 ? 6 AC1 9 ARG A 107 ? ARG A 107 . ? 1_555 ? 7 AC1 9 HOH C . ? HOH A 420 . ? 1_555 ? 8 AC1 9 HOH C . ? HOH A 442 . ? 1_555 ? 9 AC1 9 HOH C . ? HOH A 466 . ? 1_555 ? # _database_PDB_matrix.entry_id 3W8N _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 3W8N _atom_sites.fract_transf_matrix[1][1] 0.020320 _atom_sites.fract_transf_matrix[1][2] 0.011732 _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] 0.023464 _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] 0.010199 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P 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 MSE 1 1 ? ? ? A . n A 1 2 ARG 2 2 ? ? ? 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 MSE 128 128 128 MSE MSE 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 ? ? ? A . n A 1 156 GLU 156 156 ? ? ? A . n A 1 157 ARG 157 157 ? ? ? 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 176 176 176 LYS LYS A . n A 1 177 ALA 177 177 177 ALA ALA 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 MSE 193 193 193 MSE MSE 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 ? ? ? A . n A 1 208 ARG 208 208 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'NPPSFA, National Project on Protein Structural and Functional Analyses' _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 C5P 1 301 1 C5P C5P A . C 3 HOH 1 401 1 HOH TIP A . C 3 HOH 2 402 2 HOH TIP A . C 3 HOH 3 403 3 HOH TIP A . C 3 HOH 4 404 4 HOH TIP A . C 3 HOH 5 405 5 HOH TIP A . C 3 HOH 6 406 6 HOH TIP A . C 3 HOH 7 407 7 HOH TIP A . C 3 HOH 8 408 8 HOH TIP A . C 3 HOH 9 409 9 HOH TIP A . C 3 HOH 10 410 10 HOH TIP A . C 3 HOH 11 411 11 HOH TIP A . C 3 HOH 12 412 12 HOH TIP A . C 3 HOH 13 413 13 HOH TIP A . C 3 HOH 14 414 14 HOH TIP A . C 3 HOH 15 415 15 HOH TIP A . C 3 HOH 16 416 16 HOH TIP A . C 3 HOH 17 417 17 HOH TIP A . C 3 HOH 18 418 18 HOH TIP A . C 3 HOH 19 419 19 HOH TIP A . C 3 HOH 20 420 20 HOH TIP A . C 3 HOH 21 421 21 HOH TIP A . C 3 HOH 22 422 22 HOH TIP A . C 3 HOH 23 423 23 HOH TIP A . C 3 HOH 24 424 24 HOH TIP A . C 3 HOH 25 425 25 HOH TIP A . C 3 HOH 26 426 26 HOH TIP A . C 3 HOH 27 427 27 HOH TIP A . C 3 HOH 28 428 29 HOH TIP A . C 3 HOH 29 429 30 HOH TIP A . C 3 HOH 30 430 31 HOH TIP A . C 3 HOH 31 431 32 HOH TIP A . C 3 HOH 32 432 33 HOH TIP A . C 3 HOH 33 433 34 HOH TIP A . C 3 HOH 34 434 35 HOH TIP A . C 3 HOH 35 435 36 HOH TIP A . C 3 HOH 36 436 37 HOH TIP A . C 3 HOH 37 437 38 HOH TIP A . C 3 HOH 38 438 39 HOH TIP A . C 3 HOH 39 439 40 HOH TIP A . C 3 HOH 40 440 41 HOH TIP A . C 3 HOH 41 441 42 HOH TIP A . C 3 HOH 42 442 43 HOH TIP A . C 3 HOH 43 443 44 HOH TIP A . C 3 HOH 44 444 46 HOH TIP A . C 3 HOH 45 445 47 HOH TIP A . C 3 HOH 46 446 48 HOH TIP A . C 3 HOH 47 447 49 HOH TIP A . C 3 HOH 48 448 51 HOH TIP A . C 3 HOH 49 449 52 HOH TIP A . C 3 HOH 50 450 53 HOH TIP A . C 3 HOH 51 451 56 HOH TIP A . C 3 HOH 52 452 57 HOH TIP A . C 3 HOH 53 453 58 HOH TIP A . C 3 HOH 54 454 59 HOH TIP A . C 3 HOH 55 455 60 HOH TIP A . C 3 HOH 56 456 61 HOH TIP A . C 3 HOH 57 457 62 HOH TIP A . C 3 HOH 58 458 63 HOH TIP A . C 3 HOH 59 459 64 HOH TIP A . C 3 HOH 60 460 65 HOH TIP A . C 3 HOH 61 461 67 HOH TIP A . C 3 HOH 62 462 68 HOH TIP A . C 3 HOH 63 463 69 HOH TIP A . C 3 HOH 64 464 72 HOH TIP A . C 3 HOH 65 465 74 HOH TIP A . C 3 HOH 66 466 75 HOH TIP A . C 3 HOH 67 467 76 HOH TIP A . C 3 HOH 68 468 77 HOH TIP A . C 3 HOH 69 469 78 HOH TIP A . C 3 HOH 70 470 79 HOH TIP A . C 3 HOH 71 471 80 HOH TIP A . C 3 HOH 72 472 81 HOH TIP A . C 3 HOH 73 473 83 HOH TIP A . C 3 HOH 74 474 84 HOH TIP A . C 3 HOH 75 475 85 HOH TIP A . C 3 HOH 76 476 87 HOH TIP A . C 3 HOH 77 477 88 HOH TIP A . C 3 HOH 78 478 89 HOH TIP A . C 3 HOH 79 479 90 HOH TIP A . C 3 HOH 80 480 91 HOH TIP A . C 3 HOH 81 481 92 HOH TIP A . C 3 HOH 82 482 95 HOH TIP A . C 3 HOH 83 483 96 HOH TIP A . C 3 HOH 84 484 97 HOH TIP 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 128 A MSE 128 ? MET SELENOMETHIONINE 2 A MSE 193 A MSE 193 ? 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 # _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 2013-09-25 2 'Structure model' 1 1 2017-11-22 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # _diffrn_reflns.diffrn_id 1 _diffrn_reflns.pdbx_d_res_high 2.200 _diffrn_reflns.pdbx_d_res_low 50.000 _diffrn_reflns.pdbx_number_obs 26811 _diffrn_reflns.pdbx_Rmerge_I_obs 0.049 _diffrn_reflns.pdbx_Rsym_value ? _diffrn_reflns.pdbx_chi_squared 1.77 _diffrn_reflns.av_sigmaI_over_netI 20.39 _diffrn_reflns.pdbx_redundancy ? _diffrn_reflns.pdbx_percent_possible_obs 99.50 _diffrn_reflns.number 52425 _diffrn_reflns.pdbx_observed_criterion ? _diffrn_reflns.limit_h_max ? _diffrn_reflns.limit_h_min ? _diffrn_reflns.limit_k_max ? _diffrn_reflns.limit_k_min ? _diffrn_reflns.limit_l_max ? _diffrn_reflns.limit_l_min ? # loop_ _pdbx_diffrn_reflns_shell.diffrn_id _pdbx_diffrn_reflns_shell.d_res_high _pdbx_diffrn_reflns_shell.d_res_low _pdbx_diffrn_reflns_shell.number_obs _pdbx_diffrn_reflns_shell.rejects _pdbx_diffrn_reflns_shell.Rmerge_I_obs _pdbx_diffrn_reflns_shell.Rsym_value _pdbx_diffrn_reflns_shell.chi_squared _pdbx_diffrn_reflns_shell.redundancy _pdbx_diffrn_reflns_shell.percent_possible_obs 1 4.74 50.00 ? ? 0.032 ? 1.717 ? 99.40 1 3.76 4.74 ? ? 0.037 ? 1.880 ? 99.80 1 3.29 3.76 ? ? 0.046 ? 2.249 ? 99.60 1 2.99 3.29 ? ? 0.056 ? 2.145 ? 99.50 1 2.77 2.99 ? ? 0.072 ? 1.938 ? 99.50 1 2.61 2.77 ? ? 0.093 ? 1.763 ? 99.60 1 2.48 2.61 ? ? 0.124 ? 1.749 ? 99.50 1 2.37 2.48 ? ? 0.151 ? 1.533 ? 99.30 1 2.28 2.37 ? ? 0.205 ? 1.379 ? 99.40 1 2.20 2.28 ? ? 0.262 ? 1.298 ? 99.20 # _pdbx_phasing_dm.entry_id 3W8N _pdbx_phasing_dm.fom_acentric 0.580 _pdbx_phasing_dm.fom_centric 0.000 _pdbx_phasing_dm.fom 0.580 _pdbx_phasing_dm.reflns_acentric 12904 _pdbx_phasing_dm.reflns_centric 0 _pdbx_phasing_dm.reflns 12904 # loop_ _pdbx_phasing_dm_shell.d_res_high _pdbx_phasing_dm_shell.d_res_low _pdbx_phasing_dm_shell.delta_phi_final _pdbx_phasing_dm_shell.delta_phi_initial _pdbx_phasing_dm_shell.fom_acentric _pdbx_phasing_dm_shell.fom_centric _pdbx_phasing_dm_shell.fom _pdbx_phasing_dm_shell.reflns_acentric _pdbx_phasing_dm_shell.reflns_centric _pdbx_phasing_dm_shell.reflns 6.300 39.086 ? ? 0.950 ? 0.950 562 ? 562 3.900 6.300 ? ? 0.930 ? 0.930 1783 ? 1783 3.100 3.900 ? ? 0.860 ? 0.860 2241 ? 2241 2.800 3.100 ? ? 0.660 ? 0.660 2241 ? 2241 2.400 2.800 ? ? 0.380 ? 0.380 3830 ? 3830 2.200 2.400 ? ? 0.180 ? 0.180 2247 ? 2247 # _phasing.method SAD # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 SOLVE 2.13 24-Feb-2008 program 'Tom Terwilliger' terwilliger@LANL.gov phasing http://www.solve.lanl.gov/ ? ? 4 RESOLVE 2.13 6-Mar-2008 program 'Thomas C. Terwilliger' terwilliger@lanl.gov phasing http://www.solve.lanl.gov/ ? ? 5 CNS 1.3 ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns-online.org/ Fortran_77 ? 6 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 7 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 8 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? # 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 MSE A 128 ? ? 63.88 -115.84 2 1 ASP A 175 ? ? -95.52 33.41 3 1 SER A 179 ? ? -74.21 28.00 # 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 ARG 155 ? A ARG 155 4 1 Y 1 A GLU 156 ? A GLU 156 5 1 Y 1 A ARG 157 ? A ARG 157 6 1 Y 1 A ARG 207 ? A ARG 207 7 1 Y 1 A ARG 208 ? A ARG 208 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "CYTIDINE-5'-MONOPHOSPHATE" C5P 3 water HOH #