data_3PJU # _entry.id 3PJU # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3PJU RCSB RCSB062459 WWPDB D_1000062459 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3PJT . unspecified PDB 3PJV . unspecified PDB 3PJW . unspecified PDB 3PJX . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3PJU _pdbx_database_status.recvd_initial_deposition_date 2010-11-10 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sondermann, H.' 1 'Navarro, M.V.A.S.' 2 'Krasteva, P.' 3 # _citation.id primary _citation.title 'Structural Basis for c-di-GMP-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis.' _citation.journal_abbrev 'Plos Biol.' _citation.journal_volume 9 _citation.page_first e1000588 _citation.page_last e1000588 _citation.year 2011 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1544-9173 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21304926 _citation.pdbx_database_id_DOI 10.1371/journal.pbio.1000588 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Navarro, M.V.' 1 primary 'Newell, P.D.' 2 primary 'Krasteva, P.V.' 3 primary 'Chatterjee, D.' 4 primary 'Madden, D.R.' 5 primary ;O'Toole, G.A. ; 6 primary 'Sondermann, H.' 7 # _cell.entry_id 3PJU _cell.length_a 141.486 _cell.length_b 141.486 _cell.length_c 111.254 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 3PJU _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _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 'Cyclic dimeric GMP binding protein' 28293.305 1 ? ? 'UNP Residues 400-648' ? 2 non-polymer syn ;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; 690.411 1 ? ? ? ? 3 water nat water 18.015 125 ? ? ? ? # _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 ;QSLVADVGDDHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDR LMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSL QRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQ LFGEPKPWG ; _entity_poly.pdbx_seq_one_letter_code_can ;QSLVADVGDDHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDR LMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSL QRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQ LFGEPKPWG ; _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 GLN n 1 2 SER n 1 3 LEU n 1 4 VAL n 1 5 ALA n 1 6 ASP n 1 7 VAL n 1 8 GLY n 1 9 ASP n 1 10 ASP n 1 11 HIS n 1 12 HIS n 1 13 ALA n 1 14 TRP n 1 15 HIS n 1 16 ARG n 1 17 LEU n 1 18 LEU n 1 19 ASP n 1 20 GLN n 1 21 ALA n 1 22 LEU n 1 23 ASN n 1 24 GLN n 1 25 ARG n 1 26 ARG n 1 27 PHE n 1 28 GLU n 1 29 LEU n 1 30 PHE n 1 31 PHE n 1 32 GLN n 1 33 PRO n 1 34 VAL n 1 35 VAL n 1 36 ALA n 1 37 ALA n 1 38 GLN n 1 39 ASP n 1 40 THR n 1 41 GLN n 1 42 LEU n 1 43 VAL n 1 44 LEU n 1 45 HIS n 1 46 TYR n 1 47 LYS n 1 48 VAL n 1 49 LEU n 1 50 SER n 1 51 ARG n 1 52 LEU n 1 53 LEU n 1 54 ASP n 1 55 GLU n 1 56 GLN n 1 57 GLY n 1 58 GLN n 1 59 THR n 1 60 ILE n 1 61 PRO n 1 62 ALA n 1 63 GLY n 1 64 ARG n 1 65 PHE n 1 66 LEU n 1 67 PRO n 1 68 TRP n 1 69 LEU n 1 70 GLU n 1 71 ARG n 1 72 PHE n 1 73 GLY n 1 74 TRP n 1 75 THR n 1 76 ALA n 1 77 ARG n 1 78 LEU n 1 79 ASP n 1 80 ARG n 1 81 LEU n 1 82 MET n 1 83 LEU n 1 84 GLU n 1 85 ARG n 1 86 VAL n 1 87 LEU n 1 88 GLU n 1 89 GLN n 1 90 MET n 1 91 ALA n 1 92 GLY n 1 93 HIS n 1 94 GLU n 1 95 GLU n 1 96 SER n 1 97 LEU n 1 98 ALA n 1 99 LEU n 1 100 ASN n 1 101 LEU n 1 102 SER n 1 103 SER n 1 104 ALA n 1 105 THR n 1 106 LEU n 1 107 ALA n 1 108 ASP n 1 109 PRO n 1 110 GLN n 1 111 ALA n 1 112 LEU n 1 113 ASN n 1 114 LYS n 1 115 VAL n 1 116 PHE n 1 117 GLU n 1 118 ILE n 1 119 LEU n 1 120 ARG n 1 121 ALA n 1 122 HIS n 1 123 SER n 1 124 ASN n 1 125 LEU n 1 126 GLY n 1 127 ALA n 1 128 ARG n 1 129 LEU n 1 130 THR n 1 131 LEU n 1 132 GLU n 1 133 ILE n 1 134 GLY n 1 135 GLU n 1 136 GLU n 1 137 GLN n 1 138 LEU n 1 139 PRO n 1 140 GLU n 1 141 GLN n 1 142 ALA n 1 143 VAL n 1 144 LEU n 1 145 GLU n 1 146 GLN n 1 147 LEU n 1 148 THR n 1 149 ARG n 1 150 ARG n 1 151 LEU n 1 152 ARG n 1 153 GLU n 1 154 LEU n 1 155 GLY n 1 156 PHE n 1 157 SER n 1 158 LEU n 1 159 SER n 1 160 LEU n 1 161 GLN n 1 162 ARG n 1 163 PHE n 1 164 GLY n 1 165 GLY n 1 166 ARG n 1 167 PHE n 1 168 SER n 1 169 MET n 1 170 ILE n 1 171 GLY n 1 172 ASN n 1 173 LEU n 1 174 ALA n 1 175 ARG n 1 176 LEU n 1 177 GLY n 1 178 LEU n 1 179 ALA n 1 180 TYR n 1 181 LEU n 1 182 LYS n 1 183 ILE n 1 184 ASP n 1 185 GLY n 1 186 SER n 1 187 TYR n 1 188 ILE n 1 189 ARG n 1 190 ALA n 1 191 ILE n 1 192 ASP n 1 193 GLN n 1 194 GLU n 1 195 SER n 1 196 ASP n 1 197 LYS n 1 198 ARG n 1 199 LEU n 1 200 PHE n 1 201 ILE n 1 202 GLU n 1 203 ALA n 1 204 ILE n 1 205 GLN n 1 206 ARG n 1 207 ALA n 1 208 ALA n 1 209 HIS n 1 210 SER n 1 211 ILE n 1 212 ASP n 1 213 LEU n 1 214 PRO n 1 215 LEU n 1 216 ILE n 1 217 ALA n 1 218 GLU n 1 219 ARG n 1 220 VAL n 1 221 GLU n 1 222 THR n 1 223 GLU n 1 224 GLY n 1 225 GLU n 1 226 LEU n 1 227 SER n 1 228 VAL n 1 229 ILE n 1 230 ARG n 1 231 GLU n 1 232 MET n 1 233 GLY n 1 234 LEU n 1 235 TYR n 1 236 GLY n 1 237 VAL n 1 238 GLN n 1 239 GLY n 1 240 GLN n 1 241 LEU n 1 242 PHE n 1 243 GLY n 1 244 GLU n 1 245 PRO n 1 246 LYS n 1 247 PRO n 1 248 TRP n 1 249 GLY 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 'lapD, Pfl01_0131' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain Pf0-1 _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 'Pseudomonas fluorescens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 205922 _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 ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q3KK31_PSEPF _struct_ref.pdbx_db_accession Q3KK31 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;QSLVADVGDDHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDR LMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSL QRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQ LFGEPKPWG ; _struct_ref.pdbx_align_begin 400 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3PJU _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 249 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q3KK31 _struct_ref_seq.db_align_beg 400 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 648 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 400 _struct_ref_seq.pdbx_auth_seq_align_end 648 # 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 C2E non-polymer . ;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; 'c-di-GMP, Cyclic diguanosine monophosphate' 'C20 H24 N10 O14 P2' 690.411 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 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 3PJU _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _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.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '0.1 M Bis-Tris, 1.5 M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2010-02-01 _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 'Si 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9769 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'CHESS BEAMLINE A1' _diffrn_source.pdbx_synchrotron_site CHESS _diffrn_source.pdbx_synchrotron_beamline A1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9769 # _reflns.entry_id 3PJU _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F 1.0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.499 _reflns.number_obs 23191 _reflns.number_all 23260 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.499 _reflns_shell.d_res_low 2.59 _reflns_shell.percent_possible_all 97.4 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3PJU _refine.ls_number_reflns_obs 20548 _refine.ls_number_reflns_all 23260 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.19 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 35.495 _refine.ls_d_res_high 2.4991 _refine.ls_percent_reflns_obs 88.27 _refine.ls_R_factor_obs 0.1989 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1964 _refine.ls_R_factor_R_free 0.2253 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 8.48 _refine.ls_number_reflns_R_free 1742 _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 ? _refine.aniso_B[1][1] -13.2408 _refine.aniso_B[2][2] -13.2408 _refine.aniso_B[3][3] 26.4815 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.349 _refine.solvent_model_param_bsol 45.456 _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.31 _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_overall_phase_error 24.37 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1995 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 46 _refine_hist.number_atoms_solvent 125 _refine_hist.number_atoms_total 2166 _refine_hist.d_res_high 2.4991 _refine_hist.d_res_low 35.495 # 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 f_bond_d 0.008 ? ? 2091 'X-RAY DIFFRACTION' ? f_angle_d 1.239 ? ? 2838 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 23.068 ? ? 827 'X-RAY DIFFRACTION' ? f_chiral_restr 0.082 ? ? 312 'X-RAY DIFFRACTION' ? f_plane_restr 0.006 ? ? 365 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id . 2.4991 2.5726 1247 0.2726 72.00 0.3569 . . 120 . . . . 'X-RAY DIFFRACTION' . 2.5726 2.6556 1379 0.2331 79.00 0.2647 . . 125 . . . . 'X-RAY DIFFRACTION' . 2.6556 2.7505 1360 0.2317 79.00 0.2405 . . 131 . . . . 'X-RAY DIFFRACTION' . 2.7505 2.8606 1458 0.2395 83.00 0.2974 . . 131 . . . . 'X-RAY DIFFRACTION' . 2.8606 2.9907 1484 0.2352 84.00 0.2642 . . 131 . . . . 'X-RAY DIFFRACTION' . 2.9907 3.1483 1555 0.2383 89.00 0.2740 . . 140 . . . . 'X-RAY DIFFRACTION' . 3.1483 3.3454 1610 0.2087 91.00 0.2654 . . 145 . . . . 'X-RAY DIFFRACTION' . 3.3454 3.6035 1634 0.1896 92.00 0.2252 . . 153 . . . . 'X-RAY DIFFRACTION' . 3.6035 3.9657 1682 0.1766 95.00 0.2072 . . 157 . . . . 'X-RAY DIFFRACTION' . 3.9657 4.5385 1721 0.1487 96.00 0.1625 . . 159 . . . . 'X-RAY DIFFRACTION' . 4.5385 5.7142 1758 0.1671 97.00 0.1988 . . 166 . . . . 'X-RAY DIFFRACTION' . 5.7142 35.4982 1918 0.1942 99.00 0.2060 . . 184 . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 3PJU _struct.title 'Structure of Pseudomonas fluorescence LapD EAL domain complexed with c-di-GMP, P6522' _struct.pdbx_descriptor 'Cyclic dimeric GMP binding protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3PJU _struct_keywords.pdbx_keywords LYASE _struct_keywords.text 'Tim Barrel, c-di-GMP receptor, LYASE' # 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 ASP A 10 ? GLN A 24 ? ASP A 409 GLN A 423 1 ? 15 HELX_P HELX_P2 2 ALA A 62 ? PHE A 72 ? ALA A 461 PHE A 471 1 ? 11 HELX_P HELX_P3 3 TRP A 74 ? MET A 90 ? TRP A 473 MET A 489 1 ? 17 HELX_P HELX_P4 4 ALA A 91 ? HIS A 93 ? ALA A 490 HIS A 492 5 ? 3 HELX_P HELX_P5 5 SER A 102 ? ASP A 108 ? SER A 501 ASP A 507 1 ? 7 HELX_P HELX_P6 6 ASP A 108 ? HIS A 122 ? ASP A 507 HIS A 521 1 ? 15 HELX_P HELX_P7 7 SER A 123 ? ALA A 127 ? SER A 522 ALA A 526 5 ? 5 HELX_P HELX_P8 8 GLU A 136 ? LEU A 138 ? GLU A 535 LEU A 537 5 ? 3 HELX_P HELX_P9 9 GLU A 140 ? GLY A 155 ? GLU A 539 GLY A 554 1 ? 16 HELX_P HELX_P10 10 ARG A 166 ? ALA A 174 ? ARG A 565 ALA A 573 5 ? 9 HELX_P HELX_P11 11 GLY A 185 ? ILE A 188 ? GLY A 584 ILE A 587 5 ? 4 HELX_P HELX_P12 12 ALA A 190 ? ASP A 196 ? ALA A 589 ASP A 595 5 ? 7 HELX_P HELX_P13 13 LYS A 197 ? ILE A 211 ? LYS A 596 ILE A 610 1 ? 15 HELX_P HELX_P14 14 THR A 222 ? MET A 232 ? THR A 621 MET A 631 1 ? 11 HELX_P HELX_P15 15 GLY A 239 ? GLY A 243 ? GLY A 638 GLY A 642 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 10 _struct_sheet.details ? # 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 ? parallel A 3 4 ? parallel A 4 5 ? parallel A 5 6 ? parallel A 6 7 ? parallel A 7 8 ? parallel A 8 9 ? anti-parallel A 9 10 ? 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 THR A 59 ? PRO A 61 ? THR A 458 PRO A 460 A 2 VAL A 43 ? LEU A 53 ? VAL A 442 LEU A 452 A 3 LEU A 97 ? ASN A 100 ? LEU A 496 ASN A 499 A 4 LEU A 129 ? GLY A 134 ? LEU A 528 GLY A 533 A 5 SER A 157 ? PHE A 163 ? SER A 556 PHE A 562 A 6 LEU A 181 ? ILE A 183 ? LEU A 580 ILE A 582 A 7 LEU A 215 ? ALA A 217 ? LEU A 614 ALA A 616 A 8 GLY A 236 ? VAL A 237 ? GLY A 635 VAL A 636 A 9 PHE A 27 ? ALA A 36 ? PHE A 426 ALA A 435 A 10 VAL A 43 ? LEU A 53 ? VAL A 442 LEU A 452 # 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 ILE A 60 ? O ILE A 459 N LEU A 52 ? N LEU A 451 A 2 3 N VAL A 48 ? N VAL A 447 O ALA A 98 ? O ALA A 497 A 3 4 N LEU A 97 ? N LEU A 496 O THR A 130 ? O THR A 529 A 4 5 N LEU A 131 ? N LEU A 530 O SER A 159 ? O SER A 558 A 5 6 N PHE A 163 ? N PHE A 562 O LYS A 182 ? O LYS A 581 A 6 7 N LEU A 181 ? N LEU A 580 O ILE A 216 ? O ILE A 615 A 7 8 N ALA A 217 ? N ALA A 616 O GLY A 236 ? O GLY A 635 A 8 9 O VAL A 237 ? O VAL A 636 N VAL A 35 ? N VAL A 434 A 9 10 N GLU A 28 ? N GLU A 427 O ARG A 51 ? O ARG A 450 # _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 28 _struct_site.details 'BINDING SITE FOR RESIDUE C2E A 2256' # 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 28 HOH C . ? HOH A 1 . ? 1_555 ? 2 AC1 28 HOH C . ? HOH A 2 . ? 1_555 ? 3 AC1 28 HOH C . ? HOH A 31 . ? 1_555 ? 4 AC1 28 HOH C . ? HOH A 61 . ? 1_555 ? 5 AC1 28 HOH C . ? HOH A 62 . ? 1_555 ? 6 AC1 28 HOH C . ? HOH A 77 . ? 1_555 ? 7 AC1 28 GLN A 32 ? GLN A 431 . ? 1_555 ? 8 AC1 28 LYS A 47 ? LYS A 446 . ? 1_555 ? 9 AC1 28 LEU A 49 ? LEU A 448 . ? 1_555 ? 10 AC1 28 SER A 50 ? SER A 449 . ? 1_555 ? 11 AC1 28 ARG A 51 ? ARG A 450 . ? 1_555 ? 12 AC1 28 PRO A 61 ? PRO A 460 . ? 1_555 ? 13 AC1 28 ALA A 62 ? ALA A 461 . ? 1_555 ? 14 AC1 28 GLY A 63 ? GLY A 462 . ? 1_555 ? 15 AC1 28 LEU A 66 ? LEU A 465 . ? 1_555 ? 16 AC1 28 ASP A 79 ? ASP A 478 . ? 1_555 ? 17 AC1 28 MET A 82 ? MET A 481 . ? 1_555 ? 18 AC1 28 ASN A 100 ? ASN A 499 . ? 1_555 ? 19 AC1 28 GLN A 161 ? GLN A 560 . ? 1_555 ? 20 AC1 28 ARG A 162 ? ARG A 561 . ? 1_555 ? 21 AC1 28 ARG A 219 ? ARG A 618 . ? 1_555 ? 22 AC1 28 VAL A 220 ? VAL A 619 . ? 1_555 ? 23 AC1 28 GLU A 221 ? GLU A 620 . ? 1_555 ? 24 AC1 28 GLY A 239 ? GLY A 638 . ? 1_555 ? 25 AC1 28 GLN A 240 ? GLN A 639 . ? 1_555 ? 26 AC1 28 PRO A 245 ? PRO A 644 . ? 1_555 ? 27 AC1 28 HOH C . ? HOH A 663 . ? 1_555 ? 28 AC1 28 HOH C . ? HOH A 673 . ? 1_555 ? # _database_PDB_matrix.entry_id 3PJU _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 3PJU _atom_sites.fract_transf_matrix[1][1] 0.007068 _atom_sites.fract_transf_matrix[1][2] 0.004081 _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] 0.008161 _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] 0.008988 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLN 1 400 400 GLN GLN A . n A 1 2 SER 2 401 401 SER SER A . n A 1 3 LEU 3 402 402 LEU LEU A . n A 1 4 VAL 4 403 403 VAL VAL A . n A 1 5 ALA 5 404 404 ALA ALA A . n A 1 6 ASP 6 405 405 ASP ASP A . n A 1 7 VAL 7 406 406 VAL VAL A . n A 1 8 GLY 8 407 407 GLY GLY A . n A 1 9 ASP 9 408 408 ASP ASP A . n A 1 10 ASP 10 409 409 ASP ASP A . n A 1 11 HIS 11 410 410 HIS HIS A . n A 1 12 HIS 12 411 411 HIS HIS A . n A 1 13 ALA 13 412 412 ALA ALA A . n A 1 14 TRP 14 413 413 TRP TRP A . n A 1 15 HIS 15 414 414 HIS HIS A . n A 1 16 ARG 16 415 415 ARG ARG A . n A 1 17 LEU 17 416 416 LEU LEU A . n A 1 18 LEU 18 417 417 LEU LEU A . n A 1 19 ASP 19 418 418 ASP ASP A . n A 1 20 GLN 20 419 419 GLN GLN A . n A 1 21 ALA 21 420 420 ALA ALA A . n A 1 22 LEU 22 421 421 LEU LEU A . n A 1 23 ASN 23 422 422 ASN ASN A . n A 1 24 GLN 24 423 423 GLN GLN A . n A 1 25 ARG 25 424 424 ARG ARG A . n A 1 26 ARG 26 425 425 ARG ARG A . n A 1 27 PHE 27 426 426 PHE PHE A . n A 1 28 GLU 28 427 427 GLU GLU A . n A 1 29 LEU 29 428 428 LEU LEU A . n A 1 30 PHE 30 429 429 PHE PHE A . n A 1 31 PHE 31 430 430 PHE PHE A . n A 1 32 GLN 32 431 431 GLN GLN A . n A 1 33 PRO 33 432 432 PRO PRO A . n A 1 34 VAL 34 433 433 VAL VAL A . n A 1 35 VAL 35 434 434 VAL VAL A . n A 1 36 ALA 36 435 435 ALA ALA A . n A 1 37 ALA 37 436 436 ALA ALA A . n A 1 38 GLN 38 437 437 GLN GLN A . n A 1 39 ASP 39 438 438 ASP ASP A . n A 1 40 THR 40 439 439 THR THR A . n A 1 41 GLN 41 440 440 GLN GLN A . n A 1 42 LEU 42 441 441 LEU LEU A . n A 1 43 VAL 43 442 442 VAL VAL A . n A 1 44 LEU 44 443 443 LEU LEU A . n A 1 45 HIS 45 444 444 HIS HIS A . n A 1 46 TYR 46 445 445 TYR TYR A . n A 1 47 LYS 47 446 446 LYS LYS A . n A 1 48 VAL 48 447 447 VAL VAL A . n A 1 49 LEU 49 448 448 LEU LEU A . n A 1 50 SER 50 449 449 SER SER A . n A 1 51 ARG 51 450 450 ARG ARG A . n A 1 52 LEU 52 451 451 LEU LEU A . n A 1 53 LEU 53 452 452 LEU LEU A . n A 1 54 ASP 54 453 453 ASP ASP A . n A 1 55 GLU 55 454 454 GLU GLU A . n A 1 56 GLN 56 455 455 GLN GLN A . n A 1 57 GLY 57 456 456 GLY GLY A . n A 1 58 GLN 58 457 457 GLN GLN A . n A 1 59 THR 59 458 458 THR THR A . n A 1 60 ILE 60 459 459 ILE ILE A . n A 1 61 PRO 61 460 460 PRO PRO A . n A 1 62 ALA 62 461 461 ALA ALA A . n A 1 63 GLY 63 462 462 GLY GLY A . n A 1 64 ARG 64 463 463 ARG ARG A . n A 1 65 PHE 65 464 464 PHE PHE A . n A 1 66 LEU 66 465 465 LEU LEU A . n A 1 67 PRO 67 466 466 PRO PRO A . n A 1 68 TRP 68 467 467 TRP TRP A . n A 1 69 LEU 69 468 468 LEU LEU A . n A 1 70 GLU 70 469 469 GLU GLU A . n A 1 71 ARG 71 470 470 ARG ARG A . n A 1 72 PHE 72 471 471 PHE PHE A . n A 1 73 GLY 73 472 472 GLY GLY A . n A 1 74 TRP 74 473 473 TRP TRP A . n A 1 75 THR 75 474 474 THR THR A . n A 1 76 ALA 76 475 475 ALA ALA A . n A 1 77 ARG 77 476 476 ARG ARG A . n A 1 78 LEU 78 477 477 LEU LEU A . n A 1 79 ASP 79 478 478 ASP ASP A . n A 1 80 ARG 80 479 479 ARG ARG A . n A 1 81 LEU 81 480 480 LEU LEU A . n A 1 82 MET 82 481 481 MET MET A . n A 1 83 LEU 83 482 482 LEU LEU A . n A 1 84 GLU 84 483 483 GLU GLU A . n A 1 85 ARG 85 484 484 ARG ARG A . n A 1 86 VAL 86 485 485 VAL VAL A . n A 1 87 LEU 87 486 486 LEU LEU A . n A 1 88 GLU 88 487 487 GLU GLU A . n A 1 89 GLN 89 488 488 GLN GLN A . n A 1 90 MET 90 489 489 MET MET A . n A 1 91 ALA 91 490 490 ALA ALA A . n A 1 92 GLY 92 491 491 GLY GLY A . n A 1 93 HIS 93 492 492 HIS HIS A . n A 1 94 GLU 94 493 493 GLU GLU A . n A 1 95 GLU 95 494 494 GLU GLU A . n A 1 96 SER 96 495 495 SER SER A . n A 1 97 LEU 97 496 496 LEU LEU A . n A 1 98 ALA 98 497 497 ALA ALA A . n A 1 99 LEU 99 498 498 LEU LEU A . n A 1 100 ASN 100 499 499 ASN ASN A . n A 1 101 LEU 101 500 500 LEU LEU A . n A 1 102 SER 102 501 501 SER SER A . n A 1 103 SER 103 502 502 SER SER A . n A 1 104 ALA 104 503 503 ALA ALA A . n A 1 105 THR 105 504 504 THR THR A . n A 1 106 LEU 106 505 505 LEU LEU A . n A 1 107 ALA 107 506 506 ALA ALA A . n A 1 108 ASP 108 507 507 ASP ASP A . n A 1 109 PRO 109 508 508 PRO PRO A . n A 1 110 GLN 110 509 509 GLN GLN A . n A 1 111 ALA 111 510 510 ALA ALA A . n A 1 112 LEU 112 511 511 LEU LEU A . n A 1 113 ASN 113 512 512 ASN ASN A . n A 1 114 LYS 114 513 513 LYS LYS A . n A 1 115 VAL 115 514 514 VAL VAL A . n A 1 116 PHE 116 515 515 PHE PHE A . n A 1 117 GLU 117 516 516 GLU GLU A . n A 1 118 ILE 118 517 517 ILE ILE A . n A 1 119 LEU 119 518 518 LEU LEU A . n A 1 120 ARG 120 519 519 ARG ARG A . n A 1 121 ALA 121 520 520 ALA ALA A . n A 1 122 HIS 122 521 521 HIS HIS A . n A 1 123 SER 123 522 522 SER SER A . n A 1 124 ASN 124 523 523 ASN ASN A . n A 1 125 LEU 125 524 524 LEU LEU A . n A 1 126 GLY 126 525 525 GLY GLY A . n A 1 127 ALA 127 526 526 ALA ALA A . n A 1 128 ARG 128 527 527 ARG ARG A . n A 1 129 LEU 129 528 528 LEU LEU A . n A 1 130 THR 130 529 529 THR THR A . n A 1 131 LEU 131 530 530 LEU LEU A . n A 1 132 GLU 132 531 531 GLU GLU A . n A 1 133 ILE 133 532 532 ILE ILE A . n A 1 134 GLY 134 533 533 GLY GLY A . n A 1 135 GLU 135 534 534 GLU GLU A . n A 1 136 GLU 136 535 535 GLU GLU A . n A 1 137 GLN 137 536 536 GLN GLN A . n A 1 138 LEU 138 537 537 LEU LEU A . n A 1 139 PRO 139 538 538 PRO PRO A . n A 1 140 GLU 140 539 539 GLU GLU A . n A 1 141 GLN 141 540 540 GLN GLN A . n A 1 142 ALA 142 541 541 ALA ALA A . n A 1 143 VAL 143 542 542 VAL VAL A . n A 1 144 LEU 144 543 543 LEU LEU A . n A 1 145 GLU 145 544 544 GLU GLU A . n A 1 146 GLN 146 545 545 GLN GLN A . n A 1 147 LEU 147 546 546 LEU LEU A . n A 1 148 THR 148 547 547 THR THR A . n A 1 149 ARG 149 548 548 ARG ARG A . n A 1 150 ARG 150 549 549 ARG ARG A . n A 1 151 LEU 151 550 550 LEU LEU A . n A 1 152 ARG 152 551 551 ARG ARG A . n A 1 153 GLU 153 552 552 GLU GLU A . n A 1 154 LEU 154 553 553 LEU LEU A . n A 1 155 GLY 155 554 554 GLY GLY A . n A 1 156 PHE 156 555 555 PHE PHE A . n A 1 157 SER 157 556 556 SER SER A . n A 1 158 LEU 158 557 557 LEU LEU A . n A 1 159 SER 159 558 558 SER SER A . n A 1 160 LEU 160 559 559 LEU LEU A . n A 1 161 GLN 161 560 560 GLN GLN A . n A 1 162 ARG 162 561 561 ARG ARG A . n A 1 163 PHE 163 562 562 PHE PHE A . n A 1 164 GLY 164 563 563 GLY GLY A . n A 1 165 GLY 165 564 564 GLY GLY A . n A 1 166 ARG 166 565 565 ARG ARG A . n A 1 167 PHE 167 566 566 PHE PHE A . n A 1 168 SER 168 567 567 SER SER A . n A 1 169 MET 169 568 568 MET MET A . n A 1 170 ILE 170 569 569 ILE ILE A . n A 1 171 GLY 171 570 570 GLY GLY A . n A 1 172 ASN 172 571 571 ASN ASN A . n A 1 173 LEU 173 572 572 LEU LEU A . n A 1 174 ALA 174 573 573 ALA ALA A . n A 1 175 ARG 175 574 574 ARG ARG A . n A 1 176 LEU 176 575 575 LEU LEU A . n A 1 177 GLY 177 576 576 GLY GLY A . n A 1 178 LEU 178 577 577 LEU LEU A . n A 1 179 ALA 179 578 578 ALA ALA A . n A 1 180 TYR 180 579 579 TYR TYR A . n A 1 181 LEU 181 580 580 LEU LEU A . n A 1 182 LYS 182 581 581 LYS LYS A . n A 1 183 ILE 183 582 582 ILE ILE A . n A 1 184 ASP 184 583 583 ASP ASP A . n A 1 185 GLY 185 584 584 GLY GLY A . n A 1 186 SER 186 585 585 SER SER A . n A 1 187 TYR 187 586 586 TYR TYR A . n A 1 188 ILE 188 587 587 ILE ILE A . n A 1 189 ARG 189 588 588 ARG ARG A . n A 1 190 ALA 190 589 589 ALA ALA A . n A 1 191 ILE 191 590 590 ILE ILE A . n A 1 192 ASP 192 591 591 ASP ASP A . n A 1 193 GLN 193 592 592 GLN GLN A . n A 1 194 GLU 194 593 593 GLU GLU A . n A 1 195 SER 195 594 594 SER SER A . n A 1 196 ASP 196 595 595 ASP ASP A . n A 1 197 LYS 197 596 596 LYS LYS A . n A 1 198 ARG 198 597 597 ARG ARG A . n A 1 199 LEU 199 598 598 LEU LEU A . n A 1 200 PHE 200 599 599 PHE PHE A . n A 1 201 ILE 201 600 600 ILE ILE A . n A 1 202 GLU 202 601 601 GLU GLU A . n A 1 203 ALA 203 602 602 ALA ALA A . n A 1 204 ILE 204 603 603 ILE ILE A . n A 1 205 GLN 205 604 604 GLN GLN A . n A 1 206 ARG 206 605 605 ARG ARG A . n A 1 207 ALA 207 606 606 ALA ALA A . n A 1 208 ALA 208 607 607 ALA ALA A . n A 1 209 HIS 209 608 608 HIS HIS A . n A 1 210 SER 210 609 609 SER SER A . n A 1 211 ILE 211 610 610 ILE ILE A . n A 1 212 ASP 212 611 611 ASP ASP A . n A 1 213 LEU 213 612 612 LEU LEU A . n A 1 214 PRO 214 613 613 PRO PRO A . n A 1 215 LEU 215 614 614 LEU LEU A . n A 1 216 ILE 216 615 615 ILE ILE A . n A 1 217 ALA 217 616 616 ALA ALA A . n A 1 218 GLU 218 617 617 GLU GLU A . n A 1 219 ARG 219 618 618 ARG ARG A . n A 1 220 VAL 220 619 619 VAL VAL A . n A 1 221 GLU 221 620 620 GLU GLU A . n A 1 222 THR 222 621 621 THR THR A . n A 1 223 GLU 223 622 622 GLU GLU A . n A 1 224 GLY 224 623 623 GLY GLY A . n A 1 225 GLU 225 624 624 GLU GLU A . n A 1 226 LEU 226 625 625 LEU LEU A . n A 1 227 SER 227 626 626 SER SER A . n A 1 228 VAL 228 627 627 VAL VAL A . n A 1 229 ILE 229 628 628 ILE ILE A . n A 1 230 ARG 230 629 629 ARG ARG A . n A 1 231 GLU 231 630 630 GLU GLU A . n A 1 232 MET 232 631 631 MET MET A . n A 1 233 GLY 233 632 632 GLY GLY A . n A 1 234 LEU 234 633 633 LEU LEU A . n A 1 235 TYR 235 634 634 TYR TYR A . n A 1 236 GLY 236 635 635 GLY GLY A . n A 1 237 VAL 237 636 636 VAL VAL A . n A 1 238 GLN 238 637 637 GLN GLN A . n A 1 239 GLY 239 638 638 GLY GLY A . n A 1 240 GLN 240 639 639 GLN GLN A . n A 1 241 LEU 241 640 640 LEU LEU A . n A 1 242 PHE 242 641 641 PHE PHE A . n A 1 243 GLY 243 642 642 GLY GLY A . n A 1 244 GLU 244 643 643 GLU GLU A . n A 1 245 PRO 245 644 644 PRO PRO A . n A 1 246 LYS 246 645 645 LYS LYS A . n A 1 247 PRO 247 646 646 PRO PRO A . n A 1 248 TRP 248 647 647 TRP TRP A . n A 1 249 GLY 249 648 648 GLY GLY A . n # _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3740 ? 1 MORE -2 ? 1 'SSA (A^2)' 23300 ? # 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' 12_554 x,x-y,-z-1/6 0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 -18.5423333333 # 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 2011-02-09 2 'Structure model' 1 1 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 ? # _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 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 PHASER phasing . ? 2 PHENIX refinement '(phenix.refine: 1.6_289)' ? 3 XDS 'data reduction' . ? 4 XDS 'data scaling' . ? 5 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OE2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 GLU _pdbx_validate_close_contact.auth_seq_id_1 535 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 NE _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 ARG _pdbx_validate_close_contact.auth_seq_id_2 561 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.17 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 GLN _pdbx_validate_symm_contact.auth_seq_id_1 592 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 GLN _pdbx_validate_symm_contact.auth_seq_id_2 592 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 7_554 _pdbx_validate_symm_contact.dist 2.11 # 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 ASP A 507 ? ? -57.90 107.40 2 1 GLU A 593 ? ? -164.63 69.36 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 ;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; C2E 3 water HOH # 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 C2E 1 2256 2256 C2E C2E A . C 3 HOH 1 1 1 HOH HOH A . C 3 HOH 2 2 2 HOH HOH A . C 3 HOH 3 3 3 HOH HOH A . C 3 HOH 4 4 4 HOH HOH A . C 3 HOH 5 5 5 HOH HOH A . C 3 HOH 6 6 6 HOH HOH A . C 3 HOH 7 7 7 HOH HOH A . C 3 HOH 8 8 8 HOH HOH A . C 3 HOH 9 9 9 HOH HOH A . C 3 HOH 10 10 10 HOH HOH A . C 3 HOH 11 11 11 HOH HOH A . C 3 HOH 12 12 12 HOH HOH A . C 3 HOH 13 13 13 HOH HOH A . C 3 HOH 14 14 14 HOH HOH A . C 3 HOH 15 15 15 HOH HOH A . C 3 HOH 16 16 16 HOH HOH A . C 3 HOH 17 17 17 HOH HOH A . C 3 HOH 18 18 18 HOH HOH A . C 3 HOH 19 19 19 HOH HOH A . C 3 HOH 20 20 20 HOH HOH A . C 3 HOH 21 21 21 HOH HOH A . C 3 HOH 22 22 22 HOH HOH A . C 3 HOH 23 23 23 HOH HOH A . C 3 HOH 24 24 24 HOH HOH A . C 3 HOH 25 25 25 HOH HOH A . C 3 HOH 26 26 26 HOH HOH A . C 3 HOH 27 27 27 HOH HOH A . C 3 HOH 28 28 28 HOH HOH A . C 3 HOH 29 29 29 HOH HOH A . C 3 HOH 30 31 31 HOH HOH A . C 3 HOH 31 32 32 HOH HOH A . C 3 HOH 32 33 33 HOH HOH A . C 3 HOH 33 34 34 HOH HOH A . C 3 HOH 34 35 35 HOH HOH A . C 3 HOH 35 36 36 HOH HOH A . C 3 HOH 36 37 37 HOH HOH A . C 3 HOH 37 38 38 HOH HOH A . C 3 HOH 38 39 39 HOH HOH A . C 3 HOH 39 40 40 HOH HOH A . C 3 HOH 40 41 41 HOH HOH A . C 3 HOH 41 42 42 HOH HOH A . C 3 HOH 42 43 43 HOH HOH A . C 3 HOH 43 44 44 HOH HOH A . C 3 HOH 44 45 45 HOH HOH A . C 3 HOH 45 46 46 HOH HOH A . C 3 HOH 46 47 47 HOH HOH A . C 3 HOH 47 48 48 HOH HOH A . C 3 HOH 48 49 49 HOH HOH A . C 3 HOH 49 50 50 HOH HOH A . C 3 HOH 50 51 51 HOH HOH A . C 3 HOH 51 52 52 HOH HOH A . C 3 HOH 52 53 53 HOH HOH A . C 3 HOH 53 54 54 HOH HOH A . C 3 HOH 54 55 55 HOH HOH A . C 3 HOH 55 56 56 HOH HOH A . C 3 HOH 56 57 57 HOH HOH A . C 3 HOH 57 58 58 HOH HOH A . C 3 HOH 58 59 59 HOH HOH A . C 3 HOH 59 60 60 HOH HOH A . C 3 HOH 60 61 61 HOH HOH A . C 3 HOH 61 62 62 HOH HOH A . C 3 HOH 62 63 63 HOH HOH A . C 3 HOH 63 64 64 HOH HOH A . C 3 HOH 64 65 65 HOH HOH A . C 3 HOH 65 66 66 HOH HOH A . C 3 HOH 66 67 67 HOH HOH A . C 3 HOH 67 68 68 HOH HOH A . C 3 HOH 68 69 69 HOH HOH A . C 3 HOH 69 70 70 HOH HOH A . C 3 HOH 70 71 71 HOH HOH A . C 3 HOH 71 72 72 HOH HOH A . C 3 HOH 72 73 73 HOH HOH A . C 3 HOH 73 75 75 HOH HOH A . C 3 HOH 74 76 76 HOH HOH A . C 3 HOH 75 77 77 HOH HOH A . C 3 HOH 76 78 78 HOH HOH A . C 3 HOH 77 79 79 HOH HOH A . C 3 HOH 78 80 80 HOH HOH A . C 3 HOH 79 81 81 HOH HOH A . C 3 HOH 80 82 82 HOH HOH A . C 3 HOH 81 83 83 HOH HOH A . C 3 HOH 82 84 84 HOH HOH A . C 3 HOH 83 85 85 HOH HOH A . C 3 HOH 84 86 86 HOH HOH A . C 3 HOH 85 87 87 HOH HOH A . C 3 HOH 86 88 88 HOH HOH A . C 3 HOH 87 89 89 HOH HOH A . C 3 HOH 88 90 90 HOH HOH A . C 3 HOH 89 91 91 HOH HOH A . C 3 HOH 90 92 92 HOH HOH A . C 3 HOH 91 95 95 HOH HOH A . C 3 HOH 92 100 100 HOH HOH A . C 3 HOH 93 101 101 HOH HOH A . C 3 HOH 94 102 102 HOH HOH A . C 3 HOH 95 649 1 HOH HOH A . C 3 HOH 96 650 2 HOH HOH A . C 3 HOH 97 651 3 HOH HOH A . C 3 HOH 98 652 4 HOH HOH A . C 3 HOH 99 653 8 HOH HOH A . C 3 HOH 100 654 10 HOH HOH A . C 3 HOH 101 655 16 HOH HOH A . C 3 HOH 102 656 18 HOH HOH A . C 3 HOH 103 657 19 HOH HOH A . C 3 HOH 104 658 21 HOH HOH A . C 3 HOH 105 659 22 HOH HOH A . C 3 HOH 106 660 23 HOH HOH A . C 3 HOH 107 661 27 HOH HOH A . C 3 HOH 108 662 28 HOH HOH A . C 3 HOH 109 663 31 HOH HOH A . C 3 HOH 110 664 35 HOH HOH A . C 3 HOH 111 665 38 HOH HOH A . C 3 HOH 112 666 40 HOH HOH A . C 3 HOH 113 667 42 HOH HOH A . C 3 HOH 114 668 43 HOH HOH A . C 3 HOH 115 669 47 HOH HOH A . C 3 HOH 116 670 48 HOH HOH A . C 3 HOH 117 671 49 HOH HOH A . C 3 HOH 118 672 52 HOH HOH A . C 3 HOH 119 673 53 HOH HOH A . C 3 HOH 120 674 55 HOH HOH A . C 3 HOH 121 675 57 HOH HOH A . C 3 HOH 122 676 63 HOH HOH A . C 3 HOH 123 677 84 HOH HOH A . C 3 HOH 124 678 85 HOH HOH A . C 3 HOH 125 679 90 HOH HOH A . #