data_3ESJ # _entry.id 3ESJ # _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 3ESJ RCSB RCSB049713 WWPDB D_1000049713 # _pdbx_database_status.entry_id 3ESJ _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2008-10-06 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hunter, W.N.' 1 'Ramsden, N.L.' 2 # _citation.id primary _citation.title ;A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy ; _citation.journal_abbrev J.Med.Chem. _citation.journal_volume 52 _citation.page_first 2531 _citation.page_last 2542 _citation.year 2009 _citation.journal_id_ASTM JMCMAR _citation.country US _citation.journal_id_ISSN 0022-2623 _citation.journal_id_CSD 0151 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19320487 _citation.pdbx_database_id_DOI 10.1021/jm801475n # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Ramsden, N.L.' 1 primary 'Buetow, L.' 2 primary 'Dawson, A.' 3 primary 'Kemp, L.A.' 4 primary 'Ulaganathan, V.' 5 primary 'Brenk, R.' 6 primary 'Klebe, G.' 7 primary 'Hunter, W.N.' 8 # _cell.entry_id 3ESJ _cell.length_a 144.498 _cell.length_b 144.498 _cell.length_c 144.498 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 24 _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 3ESJ _symmetry.space_group_name_H-M 'I 21 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _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 '2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase' 17576.275 1 4.6.1.12 ? ? ? 2 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? 3 non-polymer syn '4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one' 305.181 1 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 5 non-polymer syn 'GERANYL DIPHOSPHATE' 314.209 1 ? ? ? ? 6 water nat water 18.015 97 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'MECPS, MECDP-synthase' # _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 ;GSHMLEMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSR ELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALL IKATK ; _entity_poly.pdbx_seq_one_letter_code_can ;GSHMLEMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSR ELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALL IKATK ; _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 GLY n 1 2 SER n 1 3 HIS n 1 4 MET n 1 5 LEU n 1 6 GLU n 1 7 MET n 1 8 ARG n 1 9 ILE n 1 10 GLY n 1 11 HIS n 1 12 GLY n 1 13 PHE n 1 14 ASP n 1 15 VAL n 1 16 HIS n 1 17 ALA n 1 18 PHE n 1 19 GLY n 1 20 GLY n 1 21 GLU n 1 22 GLY n 1 23 PRO n 1 24 ILE n 1 25 ILE n 1 26 ILE n 1 27 GLY n 1 28 GLY n 1 29 VAL n 1 30 ARG n 1 31 ILE n 1 32 PRO n 1 33 TYR n 1 34 GLU n 1 35 LYS n 1 36 GLY n 1 37 LEU n 1 38 LEU n 1 39 ALA n 1 40 HIS n 1 41 SER n 1 42 ASP n 1 43 GLY n 1 44 ASP n 1 45 VAL n 1 46 ALA n 1 47 LEU n 1 48 HIS n 1 49 ALA n 1 50 LEU n 1 51 THR n 1 52 ASP n 1 53 ALA n 1 54 LEU n 1 55 LEU n 1 56 GLY n 1 57 ALA n 1 58 ALA n 1 59 ALA n 1 60 LEU n 1 61 GLY n 1 62 ASP n 1 63 ILE n 1 64 GLY n 1 65 LYS n 1 66 LEU n 1 67 PHE n 1 68 PRO n 1 69 ASP n 1 70 THR n 1 71 ASP n 1 72 PRO n 1 73 ALA n 1 74 PHE n 1 75 LYS n 1 76 GLY n 1 77 ALA n 1 78 ASP n 1 79 SER n 1 80 ARG n 1 81 GLU n 1 82 LEU n 1 83 LEU n 1 84 ARG n 1 85 GLU n 1 86 ALA n 1 87 TRP n 1 88 ARG n 1 89 ARG n 1 90 ILE n 1 91 GLN n 1 92 ALA n 1 93 LYS n 1 94 GLY n 1 95 TYR n 1 96 THR n 1 97 LEU n 1 98 GLY n 1 99 ASN n 1 100 VAL n 1 101 ASP n 1 102 VAL n 1 103 THR n 1 104 ILE n 1 105 ILE n 1 106 ALA n 1 107 GLN n 1 108 ALA n 1 109 PRO n 1 110 LYS n 1 111 MET n 1 112 LEU n 1 113 PRO n 1 114 HIS n 1 115 ILE n 1 116 PRO n 1 117 GLN n 1 118 MET n 1 119 ARG n 1 120 VAL n 1 121 PHE n 1 122 ILE n 1 123 ALA n 1 124 GLU n 1 125 ASP n 1 126 LEU n 1 127 GLY n 1 128 CYS n 1 129 HIS n 1 130 MET n 1 131 ASP n 1 132 ASP n 1 133 VAL n 1 134 ASN n 1 135 VAL n 1 136 LYS n 1 137 ALA n 1 138 THR n 1 139 THR n 1 140 THR n 1 141 GLU n 1 142 LYS n 1 143 LEU n 1 144 GLY n 1 145 PHE n 1 146 THR n 1 147 GLY n 1 148 ARG n 1 149 GLY n 1 150 GLU n 1 151 GLY n 1 152 ILE n 1 153 ALA n 1 154 CYS n 1 155 GLU n 1 156 ALA n 1 157 VAL n 1 158 ALA n 1 159 LEU n 1 160 LEU n 1 161 ILE n 1 162 LYS n 1 163 ALA n 1 164 THR n 1 165 LYS 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 ispF _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain K12 _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 'Escherichia coli K-12' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 83333 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET15b _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code ISPF_ECOLI _struct_ref.pdbx_db_accession P62617 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREA WRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKATK ; _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 3ESJ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 7 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 165 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P62617 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 159 _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 159 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3ESJ GLY A 1 ? UNP P62617 ? ? 'EXPRESSION TAG' -5 1 1 3ESJ SER A 2 ? UNP P62617 ? ? 'EXPRESSION TAG' -4 2 1 3ESJ HIS A 3 ? UNP P62617 ? ? 'EXPRESSION TAG' -3 3 1 3ESJ MET A 4 ? UNP P62617 ? ? 'EXPRESSION TAG' -2 4 1 3ESJ LEU A 5 ? UNP P62617 ? ? 'EXPRESSION TAG' -1 5 1 3ESJ GLU A 6 ? UNP P62617 ? ? 'EXPRESSION TAG' 0 6 # 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 CC7 non-polymer . '4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one' ? 'C9 H12 N3 O7 P' 305.181 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GPP non-polymer . 'GERANYL DIPHOSPHATE' ? 'C10 H20 O7 P2' 314.209 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # _exptl.crystals_number 1 _exptl.entry_id 3ESJ _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity 0.600 _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 7.152275 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 82.802673 _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 7.5 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '2M ammonium formate, HEPES, 5% butanediol, pH 7.5, vapor diffusion, hanging drop, temperature 298K' _exptl_crystal_grow.temp_details ? _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 2003-02-01 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator SILICON _diffrn_radiation.wavelength_id 1 _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 0.9756 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_wavelength_list 0.9756 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 # _reflns.entry_id 3ESJ _reflns.d_resolution_high 2.700 _reflns.d_resolution_low 29.495 _reflns.number_obs 13946 _reflns.pdbx_Rmerge_I_obs 0.099 _reflns.pdbx_netI_over_sigmaI 5.995 _reflns.pdbx_Rsym_value 0.099 _reflns.pdbx_redundancy 14.500 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 8.9 _reflns.number_all ? _reflns.B_iso_Wilson_estimate ? _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 # 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.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.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 2.70 2.85 ? 29711 ? 0.274 2.7 0.274 ? 14.70 ? 2025 100.00 ? 1 2.85 3.02 ? 28195 ? 0.204 3.5 0.204 ? 14.80 ? 1907 100.00 ? 2 3.02 3.23 ? 26472 ? 0.154 4.4 0.154 ? 14.80 ? 1791 100.00 ? 3 3.23 3.49 ? 24457 ? 0.121 5.5 0.121 ? 14.70 ? 1659 100.00 ? 4 3.49 3.82 ? 22821 ? 0.102 6.5 0.102 ? 14.70 ? 1553 100.00 ? 5 3.82 4.27 ? 20737 ? 0.086 7.3 0.086 ? 14.60 ? 1416 100.00 ? 6 4.27 4.93 ? 17804 ? 0.076 8.2 0.076 ? 14.50 ? 1227 100.00 ? 7 4.93 6.04 ? 15159 ? 0.073 8.2 0.073 ? 14.20 ? 1071 100.00 ? 8 6.04 8.54 ? 11211 ? 0.067 8.7 0.067 ? 13.50 ? 830 100.00 ? 9 8.54 29.50 ? 5448 ? 0.062 9.5 0.062 ? 11.70 ? 467 97.80 ? 10 # _refine.entry_id 3ESJ _refine.ls_d_res_high 2.700 _refine.ls_d_res_low 24.69 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.930 _refine.ls_number_reflns_obs 13786 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.ls_R_factor_obs 0.186 _refine.ls_R_factor_R_work 0.184 _refine.ls_wR_factor_R_work 0.185 _refine.ls_R_factor_R_free 0.218 _refine.ls_wR_factor_R_free 0.220 _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 690 _refine.B_iso_mean 40.065 _refine.correlation_coeff_Fo_to_Fc 0.941 _refine.correlation_coeff_Fo_to_Fc_free 0.917 _refine.overall_SU_R_Cruickshank_DPI 0.212 _refine.overall_SU_R_free 0.193 _refine.pdbx_overall_ESU_R 0.212 _refine.pdbx_overall_ESU_R_Free 0.193 _refine.overall_SU_ML 0.127 _refine.overall_SU_B 6.281 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.overall_FOM_work_R_set 0.854 _refine.B_iso_max 98.13 _refine.B_iso_min 2.81 _refine.occupancy_max 1.00 _refine.occupancy_min 0.33 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 13795 _refine.ls_R_factor_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model 1GX1 _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _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 1215 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 41 _refine_hist.number_atoms_solvent 97 _refine_hist.number_atoms_total 1353 _refine_hist.d_res_high 2.700 _refine_hist.d_res_low 24.69 # 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_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 1277 0.013 0.022 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1730 1.551 2.013 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 161 6.139 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 50 35.792 23.800 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 211 19.381 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 8 16.282 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 195 0.091 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 942 0.004 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 596 0.237 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 844 0.319 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 80 0.131 0.200 ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 1 0.058 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 62 0.341 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 14 0.183 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined 1 0.015 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 811 0.999 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1265 1.631 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 505 1.764 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 465 2.979 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.701 _refine_ls_shell.d_res_low 2.771 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 100.000 _refine_ls_shell.number_reflns_R_work 834 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.263 _refine_ls_shell.R_factor_R_free 0.320 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 47 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 881 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3ESJ _struct.title 'Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand' _struct.pdbx_descriptor '2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (E.C.4.6.1.12)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3ESJ _struct_keywords.text 'MECDP-synthase, Isoprene biosynthesis, Lyase, Magnesium, Manganese, Metal-binding' _struct_keywords.pdbx_keywords 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 ? D N N 4 ? E N N 5 ? F N N 6 ? # _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 44 ? ALA A 58 ? ASP A 38 ALA A 52 1 ? 15 HELX_P HELX_P2 2 ASP A 62 ? PHE A 67 ? ASP A 56 PHE A 61 1 ? 6 HELX_P HELX_P3 3 ASP A 71 ? LYS A 75 ? ASP A 65 LYS A 69 5 ? 5 HELX_P HELX_P4 4 ASP A 78 ? LYS A 93 ? ASP A 72 LYS A 87 1 ? 16 HELX_P HELX_P5 5 MET A 111 ? PRO A 113 ? MET A 105 PRO A 107 5 ? 3 HELX_P HELX_P6 6 HIS A 114 ? LEU A 126 ? HIS A 108 LEU A 120 1 ? 13 HELX_P HELX_P7 7 HIS A 129 ? ASP A 131 ? HIS A 123 ASP A 125 5 ? 3 HELX_P HELX_P8 8 LEU A 143 ? ARG A 148 ? LEU A 137 ARG A 142 1 ? 6 # _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 metalc1 metalc ? ? A ASP 14 OD2 ? ? ? 1_555 B ZN . ZN ? ? A ASP 8 A ZN 900 1_555 ? ? ? ? ? ? ? 2.034 ? metalc2 metalc ? ? A HIS 16 NE2 ? ? ? 1_555 B ZN . ZN ? ? A HIS 10 A ZN 900 1_555 ? ? ? ? ? ? ? 2.001 ? metalc3 metalc ? ? A HIS 48 ND1 ? ? ? 1_555 B ZN . ZN ? ? A HIS 42 A ZN 900 1_555 ? ? ? ? ? ? ? 2.093 ? metalc4 metalc ? ? A GLU 155 OE1 ? ? ? 1_555 D MG . MG ? ? A GLU 149 A MG 903 1_555 ? ? ? ? ? ? ? 2.324 ? metalc5 metalc ? ? A GLU 155 OE2 ? ? ? 1_555 D MG . MG ? ? A GLU 149 A MG 903 1_555 ? ? ? ? ? ? ? 2.029 ? metalc6 metalc ? ? B ZN . ZN ? ? ? 1_555 F HOH . O ? ? A ZN 900 A HOH 922 1_555 ? ? ? ? ? ? ? 2.344 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 ALA 108 A . ? ALA 102 A PRO 109 A ? PRO 103 A 1 0.34 2 THR 164 A . ? THR 158 A LYS 165 A ? LYS 159 A 1 -2.96 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 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 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? parallel B 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 GLY A 36 ? LEU A 37 ? GLY A 30 LEU A 31 A 2 LEU A 5 ? GLY A 19 ? LEU A -1 GLY A 13 A 3 GLY A 151 ? ALA A 163 ? GLY A 145 ALA A 157 A 4 TYR A 95 ? ILE A 105 ? TYR A 89 ILE A 99 A 5 VAL A 133 ? THR A 138 ? VAL A 127 THR A 132 B 1 ILE A 24 ? ILE A 26 ? ILE A 18 ILE A 20 B 2 VAL A 29 ? ILE A 31 ? VAL A 23 ILE A 25 # 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 GLY A 36 ? O GLY A 30 N GLY A 19 ? N GLY A 13 A 2 3 N ARG A 8 ? N ARG A 2 O LEU A 160 ? O LEU A 154 A 3 4 O ALA A 153 ? O ALA A 147 N ILE A 105 ? N ILE A 99 A 4 5 N ILE A 104 ? N ILE A 98 O LYS A 136 ? O LYS A 130 B 1 2 N ILE A 24 ? N ILE A 18 O ILE A 31 ? O ILE A 25 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A 900' AC2 Software ? ? ? ? 10 'BINDING SITE FOR RESIDUE CC7 A 901' AC3 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE MG A 903' AC4 Software ? ? ? ? 15 'BINDING SITE FOR RESIDUE GPP A 904' # 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 4 ASP A 14 ? ASP A 8 . ? 1_555 ? 2 AC1 4 HIS A 16 ? HIS A 10 . ? 1_555 ? 3 AC1 4 HIS A 48 ? HIS A 42 . ? 1_555 ? 4 AC1 4 HOH F . ? HOH A 922 . ? 1_555 ? 5 AC2 10 ASP A 62 ? ASP A 56 . ? 9_555 ? 6 AC2 10 GLY A 64 ? GLY A 58 . ? 9_555 ? 7 AC2 10 ASP A 69 ? ASP A 63 . ? 9_555 ? 8 AC2 10 ALA A 106 ? ALA A 100 . ? 1_555 ? 9 AC2 10 PRO A 109 ? PRO A 103 . ? 1_555 ? 10 AC2 10 LYS A 110 ? LYS A 104 . ? 1_555 ? 11 AC2 10 MET A 111 ? MET A 105 . ? 1_555 ? 12 AC2 10 LEU A 112 ? LEU A 106 . ? 1_555 ? 13 AC2 10 ALA A 137 ? ALA A 131 . ? 1_555 ? 14 AC2 10 HOH F . ? HOH A 1001 . ? 1_555 ? 15 AC3 3 GLU A 155 ? GLU A 149 . ? 5_555 ? 16 AC3 3 GLU A 155 ? GLU A 149 . ? 1_555 ? 17 AC3 3 GLU A 155 ? GLU A 149 . ? 9_555 ? 18 AC4 15 PHE A 13 ? PHE A 7 . ? 9_555 ? 19 AC4 15 PHE A 13 ? PHE A 7 . ? 1_555 ? 20 AC4 15 ILE A 105 ? ILE A 99 . ? 1_555 ? 21 AC4 15 LEU A 143 ? LEU A 137 . ? 1_555 ? 22 AC4 15 GLY A 144 ? GLY A 138 . ? 1_555 ? 23 AC4 15 GLY A 144 ? GLY A 138 . ? 5_555 ? 24 AC4 15 GLY A 144 ? GLY A 138 . ? 9_555 ? 25 AC4 15 PHE A 145 ? PHE A 139 . ? 1_555 ? 26 AC4 15 PHE A 145 ? PHE A 139 . ? 5_555 ? 27 AC4 15 PHE A 145 ? PHE A 139 . ? 9_555 ? 28 AC4 15 THR A 146 ? THR A 140 . ? 1_555 ? 29 AC4 15 ARG A 148 ? ARG A 142 . ? 9_555 ? 30 AC4 15 ARG A 148 ? ARG A 142 . ? 5_555 ? 31 AC4 15 ARG A 148 ? ARG A 142 . ? 1_555 ? 32 AC4 15 GLU A 155 ? GLU A 149 . ? 1_555 ? # _atom_sites.entry_id 3ESJ _atom_sites.fract_transf_matrix[1][1] 0.006921 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.006921 _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] 0.006921 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P S ZN # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 -5 ? ? ? A . n A 1 2 SER 2 -4 ? ? ? A . n A 1 3 HIS 3 -3 ? ? ? A . n A 1 4 MET 4 -2 -2 MET MET A . n A 1 5 LEU 5 -1 -1 LEU LEU A . n A 1 6 GLU 6 0 0 GLU GLU A . n A 1 7 MET 7 1 1 MET MET A . n A 1 8 ARG 8 2 2 ARG ARG A . n A 1 9 ILE 9 3 3 ILE ILE A . n A 1 10 GLY 10 4 4 GLY GLY A . n A 1 11 HIS 11 5 5 HIS HIS A . n A 1 12 GLY 12 6 6 GLY GLY A . n A 1 13 PHE 13 7 7 PHE PHE A . n A 1 14 ASP 14 8 8 ASP ASP A . n A 1 15 VAL 15 9 9 VAL VAL A . n A 1 16 HIS 16 10 10 HIS HIS A . n A 1 17 ALA 17 11 11 ALA ALA A . n A 1 18 PHE 18 12 12 PHE PHE A . n A 1 19 GLY 19 13 13 GLY GLY A . n A 1 20 GLY 20 14 14 GLY GLY A . n A 1 21 GLU 21 15 15 GLU GLU A . n A 1 22 GLY 22 16 16 GLY GLY A . n A 1 23 PRO 23 17 17 PRO PRO A . n A 1 24 ILE 24 18 18 ILE ILE A . n A 1 25 ILE 25 19 19 ILE ILE A . n A 1 26 ILE 26 20 20 ILE ILE A . n A 1 27 GLY 27 21 21 GLY GLY A . n A 1 28 GLY 28 22 22 GLY GLY A . n A 1 29 VAL 29 23 23 VAL VAL A . n A 1 30 ARG 30 24 24 ARG ARG A . n A 1 31 ILE 31 25 25 ILE ILE A . n A 1 32 PRO 32 26 26 PRO PRO A . n A 1 33 TYR 33 27 27 TYR TYR A . n A 1 34 GLU 34 28 28 GLU GLU A . n A 1 35 LYS 35 29 29 LYS LYS A . n A 1 36 GLY 36 30 30 GLY GLY A . n A 1 37 LEU 37 31 31 LEU LEU A . n A 1 38 LEU 38 32 32 LEU LEU A . n A 1 39 ALA 39 33 33 ALA ALA A . n A 1 40 HIS 40 34 34 HIS HIS A . n A 1 41 SER 41 35 35 SER SER A . n A 1 42 ASP 42 36 36 ASP ASP A . n A 1 43 GLY 43 37 37 GLY GLY A . n A 1 44 ASP 44 38 38 ASP ASP A . n A 1 45 VAL 45 39 39 VAL VAL A . n A 1 46 ALA 46 40 40 ALA ALA A . n A 1 47 LEU 47 41 41 LEU LEU A . n A 1 48 HIS 48 42 42 HIS HIS A . n A 1 49 ALA 49 43 43 ALA ALA A . n A 1 50 LEU 50 44 44 LEU LEU A . n A 1 51 THR 51 45 45 THR THR A . n A 1 52 ASP 52 46 46 ASP ASP A . n A 1 53 ALA 53 47 47 ALA ALA A . n A 1 54 LEU 54 48 48 LEU LEU A . n A 1 55 LEU 55 49 49 LEU LEU A . n A 1 56 GLY 56 50 50 GLY GLY A . n A 1 57 ALA 57 51 51 ALA ALA A . n A 1 58 ALA 58 52 52 ALA ALA A . n A 1 59 ALA 59 53 53 ALA ALA A . n A 1 60 LEU 60 54 54 LEU LEU A . n A 1 61 GLY 61 55 55 GLY GLY A . n A 1 62 ASP 62 56 56 ASP ASP A . n A 1 63 ILE 63 57 57 ILE ILE A . n A 1 64 GLY 64 58 58 GLY GLY A . n A 1 65 LYS 65 59 59 LYS LYS A . n A 1 66 LEU 66 60 60 LEU LEU A . n A 1 67 PHE 67 61 61 PHE PHE A . n A 1 68 PRO 68 62 62 PRO PRO A . n A 1 69 ASP 69 63 63 ASP ASP A . n A 1 70 THR 70 64 64 THR THR A . n A 1 71 ASP 71 65 65 ASP ASP A . n A 1 72 PRO 72 66 66 PRO PRO A . n A 1 73 ALA 73 67 67 ALA ALA A . n A 1 74 PHE 74 68 68 PHE PHE A . n A 1 75 LYS 75 69 69 LYS LYS A . n A 1 76 GLY 76 70 70 GLY GLY A . n A 1 77 ALA 77 71 71 ALA ALA A . n A 1 78 ASP 78 72 72 ASP ASP A . n A 1 79 SER 79 73 73 SER SER A . n A 1 80 ARG 80 74 74 ARG ARG A . n A 1 81 GLU 81 75 75 GLU GLU A . n A 1 82 LEU 82 76 76 LEU LEU A . n A 1 83 LEU 83 77 77 LEU LEU A . n A 1 84 ARG 84 78 78 ARG ARG A . n A 1 85 GLU 85 79 79 GLU GLU A . n A 1 86 ALA 86 80 80 ALA ALA A . n A 1 87 TRP 87 81 81 TRP TRP A . n A 1 88 ARG 88 82 82 ARG ARG A . n A 1 89 ARG 89 83 83 ARG ARG A . n A 1 90 ILE 90 84 84 ILE ILE A . n A 1 91 GLN 91 85 85 GLN GLN A . n A 1 92 ALA 92 86 86 ALA ALA A . n A 1 93 LYS 93 87 87 LYS LYS A . n A 1 94 GLY 94 88 88 GLY GLY A . n A 1 95 TYR 95 89 89 TYR TYR A . n A 1 96 THR 96 90 90 THR THR A . n A 1 97 LEU 97 91 91 LEU LEU A . n A 1 98 GLY 98 92 92 GLY GLY A . n A 1 99 ASN 99 93 93 ASN ASN A . n A 1 100 VAL 100 94 94 VAL VAL A . n A 1 101 ASP 101 95 95 ASP ASP A . n A 1 102 VAL 102 96 96 VAL VAL A . n A 1 103 THR 103 97 97 THR THR A . n A 1 104 ILE 104 98 98 ILE ILE A . n A 1 105 ILE 105 99 99 ILE ILE A . n A 1 106 ALA 106 100 100 ALA ALA A . n A 1 107 GLN 107 101 101 GLN GLN A . n A 1 108 ALA 108 102 102 ALA ALA A . n A 1 109 PRO 109 103 103 PRO PRO A . n A 1 110 LYS 110 104 104 LYS LYS A . n A 1 111 MET 111 105 105 MET MET A . n A 1 112 LEU 112 106 106 LEU LEU A . n A 1 113 PRO 113 107 107 PRO PRO A . n A 1 114 HIS 114 108 108 HIS HIS A . n A 1 115 ILE 115 109 109 ILE ILE A . n A 1 116 PRO 116 110 110 PRO PRO A . n A 1 117 GLN 117 111 111 GLN GLN A . n A 1 118 MET 118 112 112 MET MET A . n A 1 119 ARG 119 113 113 ARG ARG A . n A 1 120 VAL 120 114 114 VAL VAL A . n A 1 121 PHE 121 115 115 PHE PHE A . n A 1 122 ILE 122 116 116 ILE ILE A . n A 1 123 ALA 123 117 117 ALA ALA A . n A 1 124 GLU 124 118 118 GLU GLU A . n A 1 125 ASP 125 119 119 ASP ASP A . n A 1 126 LEU 126 120 120 LEU LEU A . n A 1 127 GLY 127 121 121 GLY GLY A . n A 1 128 CYS 128 122 122 CYS CYS A . n A 1 129 HIS 129 123 123 HIS HIS A . n A 1 130 MET 130 124 124 MET MET A . n A 1 131 ASP 131 125 125 ASP ASP A . n A 1 132 ASP 132 126 126 ASP ASP A . n A 1 133 VAL 133 127 127 VAL VAL A . n A 1 134 ASN 134 128 128 ASN ASN A . n A 1 135 VAL 135 129 129 VAL VAL A . n A 1 136 LYS 136 130 130 LYS LYS A . n A 1 137 ALA 137 131 131 ALA ALA A . n A 1 138 THR 138 132 132 THR THR A . n A 1 139 THR 139 133 133 THR THR A . n A 1 140 THR 140 134 134 THR THR A . n A 1 141 GLU 141 135 135 GLU GLU A . n A 1 142 LYS 142 136 136 LYS LYS A . n A 1 143 LEU 143 137 137 LEU LEU A . n A 1 144 GLY 144 138 138 GLY GLY A . n A 1 145 PHE 145 139 139 PHE PHE A . n A 1 146 THR 146 140 140 THR THR A . n A 1 147 GLY 147 141 141 GLY GLY A . n A 1 148 ARG 148 142 142 ARG ARG A . n A 1 149 GLY 149 143 143 GLY GLY A . n A 1 150 GLU 150 144 144 GLU GLU A . n A 1 151 GLY 151 145 145 GLY GLY A . n A 1 152 ILE 152 146 146 ILE ILE A . n A 1 153 ALA 153 147 147 ALA ALA A . n A 1 154 CYS 154 148 148 CYS CYS A . n A 1 155 GLU 155 149 149 GLU GLU A . n A 1 156 ALA 156 150 150 ALA ALA A . n A 1 157 VAL 157 151 151 VAL VAL A . n A 1 158 ALA 158 152 152 ALA ALA A . n A 1 159 LEU 159 153 153 LEU LEU A . n A 1 160 LEU 160 154 154 LEU LEU A . n A 1 161 ILE 161 155 155 ILE ILE A . n A 1 162 LYS 162 156 156 LYS LYS A . n A 1 163 ALA 163 157 157 ALA ALA A . n A 1 164 THR 164 158 158 THR THR A . n A 1 165 LYS 165 159 159 LYS LYS 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 trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # 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)' 8770 ? 1 MORE -172 ? 1 'SSA (A^2)' 17180 ? # 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' 5_555 z,x,y 0.0000000000 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 3 'crystal symmetry operation' 9_555 y,z,x 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A MG 903 ? D MG . 2 1 A GPP 904 ? E GPP . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OD2 ? A ASP 14 ? A ASP 8 ? 1_555 ZN ? B ZN . ? A ZN 900 ? 1_555 NE2 ? A HIS 16 ? A HIS 10 ? 1_555 101.2 ? 2 OD2 ? A ASP 14 ? A ASP 8 ? 1_555 ZN ? B ZN . ? A ZN 900 ? 1_555 ND1 ? A HIS 48 ? A HIS 42 ? 1_555 95.8 ? 3 NE2 ? A HIS 16 ? A HIS 10 ? 1_555 ZN ? B ZN . ? A ZN 900 ? 1_555 ND1 ? A HIS 48 ? A HIS 42 ? 1_555 108.9 ? 4 OD2 ? A ASP 14 ? A ASP 8 ? 1_555 ZN ? B ZN . ? A ZN 900 ? 1_555 O ? F HOH . ? A HOH 922 ? 1_555 143.8 ? 5 NE2 ? A HIS 16 ? A HIS 10 ? 1_555 ZN ? B ZN . ? A ZN 900 ? 1_555 O ? F HOH . ? A HOH 922 ? 1_555 101.4 ? 6 ND1 ? A HIS 48 ? A HIS 42 ? 1_555 ZN ? B ZN . ? A ZN 900 ? 1_555 O ? F HOH . ? A HOH 922 ? 1_555 103.0 ? 7 OE1 ? A GLU 155 ? A GLU 149 ? 1_555 MG ? D MG . ? A MG 903 ? 1_555 OE2 ? A GLU 155 ? A GLU 149 ? 1_555 59.0 ? # 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 2009-08-25 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' # _phasing.method MR # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal MOSFLM . ? package 'Andrew G.W. Leslie' andrew@mrc-lmb.cam.ac.uk 'data reduction' http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ ? ? 1 SCALA 3.1.20 6/11/2002 other 'Phil R. Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/scala.html Fortran_77 ? 2 AMoRE . ? program 'Jorge Navaza' ccp4@ccp4.ac.uk phasing http://www.ccp4.ac.uk/ Fortran_77 ? 3 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU A 15 ? ? -173.30 -172.92 2 1 ASP A 36 ? ? -39.59 -30.43 3 1 ASP A 38 ? ? -68.64 94.79 # 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 GLY -5 ? A GLY 1 2 1 Y 1 A SER -4 ? A SER 2 3 1 Y 1 A HIS -3 ? A HIS 3 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ZINC ION' ZN 3 '4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one' CC7 4 'MAGNESIUM ION' MG 5 'GERANYL DIPHOSPHATE' GPP 6 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 ZN 1 900 900 ZN ZN A . C 3 CC7 1 901 901 CC7 CC7 A . D 4 MG 1 903 903 MG MG A . E 5 GPP 1 904 904 GPP GPP A . F 6 HOH 1 905 905 HOH HOH A . F 6 HOH 2 906 906 HOH HOH A . F 6 HOH 3 907 907 HOH HOH A . F 6 HOH 4 908 908 HOH HOH A . F 6 HOH 5 909 909 HOH HOH A . F 6 HOH 6 910 910 HOH HOH A . F 6 HOH 7 911 911 HOH HOH A . F 6 HOH 8 912 912 HOH HOH A . F 6 HOH 9 913 913 HOH HOH A . F 6 HOH 10 914 914 HOH HOH A . F 6 HOH 11 915 915 HOH HOH A . F 6 HOH 12 916 916 HOH HOH A . F 6 HOH 13 917 917 HOH HOH A . F 6 HOH 14 918 918 HOH HOH A . F 6 HOH 15 919 919 HOH HOH A . F 6 HOH 16 920 920 HOH HOH A . F 6 HOH 17 921 921 HOH HOH A . F 6 HOH 18 922 922 HOH HOH A . F 6 HOH 19 923 923 HOH HOH A . F 6 HOH 20 924 924 HOH HOH A . F 6 HOH 21 925 925 HOH HOH A . F 6 HOH 22 926 926 HOH HOH A . F 6 HOH 23 927 927 HOH HOH A . F 6 HOH 24 928 928 HOH HOH A . F 6 HOH 25 929 929 HOH HOH A . F 6 HOH 26 930 930 HOH HOH A . F 6 HOH 27 931 931 HOH HOH A . F 6 HOH 28 932 932 HOH HOH A . F 6 HOH 29 933 933 HOH HOH A . F 6 HOH 30 934 934 HOH HOH A . F 6 HOH 31 935 935 HOH HOH A . F 6 HOH 32 936 936 HOH HOH A . F 6 HOH 33 937 937 HOH HOH A . F 6 HOH 34 938 938 HOH HOH A . F 6 HOH 35 939 939 HOH HOH A . F 6 HOH 36 940 940 HOH HOH A . F 6 HOH 37 941 941 HOH HOH A . F 6 HOH 38 942 942 HOH HOH A . F 6 HOH 39 943 943 HOH HOH A . F 6 HOH 40 944 944 HOH HOH A . F 6 HOH 41 945 945 HOH HOH A . F 6 HOH 42 946 946 HOH HOH A . F 6 HOH 43 947 947 HOH HOH A . F 6 HOH 44 948 948 HOH HOH A . F 6 HOH 45 949 949 HOH HOH A . F 6 HOH 46 950 950 HOH HOH A . F 6 HOH 47 951 951 HOH HOH A . F 6 HOH 48 952 952 HOH HOH A . F 6 HOH 49 953 953 HOH HOH A . F 6 HOH 50 954 954 HOH HOH A . F 6 HOH 51 955 955 HOH HOH A . F 6 HOH 52 956 956 HOH HOH A . F 6 HOH 53 957 957 HOH HOH A . F 6 HOH 54 958 958 HOH HOH A . F 6 HOH 55 959 959 HOH HOH A . F 6 HOH 56 960 960 HOH HOH A . F 6 HOH 57 961 961 HOH HOH A . F 6 HOH 58 962 962 HOH HOH A . F 6 HOH 59 963 963 HOH HOH A . F 6 HOH 60 964 964 HOH HOH A . F 6 HOH 61 965 965 HOH HOH A . F 6 HOH 62 966 966 HOH HOH A . F 6 HOH 63 967 967 HOH HOH A . F 6 HOH 64 968 968 HOH HOH A . F 6 HOH 65 969 969 HOH HOH A . F 6 HOH 66 970 970 HOH HOH A . F 6 HOH 67 971 971 HOH HOH A . F 6 HOH 68 972 972 HOH HOH A . F 6 HOH 69 973 973 HOH HOH A . F 6 HOH 70 974 974 HOH HOH A . F 6 HOH 71 975 975 HOH HOH A . F 6 HOH 72 976 976 HOH HOH A . F 6 HOH 73 977 977 HOH HOH A . F 6 HOH 74 978 978 HOH HOH A . F 6 HOH 75 979 979 HOH HOH A . F 6 HOH 76 980 980 HOH HOH A . F 6 HOH 77 981 981 HOH HOH A . F 6 HOH 78 982 982 HOH HOH A . F 6 HOH 79 983 983 HOH HOH A . F 6 HOH 80 984 984 HOH HOH A . F 6 HOH 81 985 985 HOH HOH A . F 6 HOH 82 986 986 HOH HOH A . F 6 HOH 83 987 987 HOH HOH A . F 6 HOH 84 988 988 HOH HOH A . F 6 HOH 85 989 989 HOH HOH A . F 6 HOH 86 990 990 HOH HOH A . F 6 HOH 87 991 991 HOH HOH A . F 6 HOH 88 992 992 HOH HOH A . F 6 HOH 89 993 993 HOH HOH A . F 6 HOH 90 994 994 HOH HOH A . F 6 HOH 91 995 995 HOH HOH A . F 6 HOH 92 996 996 HOH HOH A . F 6 HOH 93 997 997 HOH HOH A . F 6 HOH 94 998 998 HOH HOH A . F 6 HOH 95 999 999 HOH HOH A . F 6 HOH 96 1000 1000 HOH HOH A . F 6 HOH 97 1001 1001 HOH HOH A . #