data_1KNJ # _entry.id 1KNJ # _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 1KNJ RCSB RCSB015145 WWPDB D_1000015145 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1KNK _pdbx_database_related.details ;Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF) from E. coli involved in mevalonate-independent isoprenoid biosynthesis ; _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1KNJ _pdbx_database_status.recvd_initial_deposition_date 2001-12-18 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Richard, S.B.' 1 'Ferrer, J.L.' 2 'Bowman, M.E.' 3 'Lillo, A.M.' 4 'Tetzlaff, C.N.' 5 'Cane, D.E.' 6 'Noel, J.P.' 7 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway. ; J.Biol.Chem. 277 8667 8672 2002 JBCHA3 US 0021-9258 0071 ? 11786530 10.1074/jbc.C100739200 1 ;Structure of 4-diphosphocytidyl-2-C-methylerythritol Synthetase Involved in Mevalonate-Independent Isoprenoid Biosynthesis ; Nat.Struct.Biol. 8 641 648 2001 NSBIEW US 1072-8368 2024 ? ? 10.1038/89691 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Richard, S.B.' 1 primary 'Ferrer, J.L.' 2 primary 'Bowman, M.E.' 3 primary 'Lillo, A.M.' 4 primary 'Tetzlaff, C.N.' 5 primary 'Cane, D.E.' 6 primary 'Noel, J.P.' 7 1 'Richard, S.B.' 8 1 'Bowman, M.E.' 9 1 'Kwiatkowski, W.' 10 1 'Kang, I.' 11 1 'Chow, C.' 12 1 'Lillo, A.M.' 13 1 'Cane, D.E.' 14 1 'Noel, J.P.' 15 # _cell.entry_id 1KNJ _cell.length_a 144.254 _cell.length_b 144.254 _cell.length_c 144.254 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KNJ _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 # 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 '2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase' 17108.113 1 ? ? ? ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 1 ? ? ? ? 3 non-polymer syn "CYTIDINE-5'-MONOPHOSPHATE" 323.197 1 ? ? ? ? 4 non-polymer syn '2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE' 278.091 1 ? ? ? ? 5 water nat water 18.015 22 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name MECPS # _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)RIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSREL LREAWRRIQAKGYTLGNVDVTIIAQAPK(MSE)LPHIPQ(MSE)RVFIAEDLGCH(MSE)DDVNVKATTTEKLGFTGRGE GIACEAVALLIKATK ; _entity_poly.pdbx_seq_one_letter_code_can ;MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREA WRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKATK ; _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 MSE n 1 2 ARG n 1 3 ILE n 1 4 GLY n 1 5 HIS n 1 6 GLY n 1 7 PHE n 1 8 ASP n 1 9 VAL n 1 10 HIS n 1 11 ALA n 1 12 PHE n 1 13 GLY n 1 14 GLY n 1 15 GLU n 1 16 GLY n 1 17 PRO n 1 18 ILE n 1 19 ILE n 1 20 ILE n 1 21 GLY n 1 22 GLY n 1 23 VAL n 1 24 ARG n 1 25 ILE n 1 26 PRO n 1 27 TYR n 1 28 GLU n 1 29 LYS n 1 30 GLY n 1 31 LEU n 1 32 LEU n 1 33 ALA n 1 34 HIS n 1 35 SER n 1 36 ASP n 1 37 GLY n 1 38 ASP n 1 39 VAL n 1 40 ALA n 1 41 LEU n 1 42 HIS n 1 43 ALA n 1 44 LEU n 1 45 THR n 1 46 ASP n 1 47 ALA n 1 48 LEU n 1 49 LEU n 1 50 GLY n 1 51 ALA n 1 52 ALA n 1 53 ALA n 1 54 LEU n 1 55 GLY n 1 56 ASP n 1 57 ILE n 1 58 GLY n 1 59 LYS n 1 60 LEU n 1 61 PHE n 1 62 PRO n 1 63 ASP n 1 64 THR n 1 65 ASP n 1 66 PRO n 1 67 ALA n 1 68 PHE n 1 69 LYS n 1 70 GLY n 1 71 ALA n 1 72 ASP n 1 73 SER n 1 74 ARG n 1 75 GLU n 1 76 LEU n 1 77 LEU n 1 78 ARG n 1 79 GLU n 1 80 ALA n 1 81 TRP n 1 82 ARG n 1 83 ARG n 1 84 ILE n 1 85 GLN n 1 86 ALA n 1 87 LYS n 1 88 GLY n 1 89 TYR n 1 90 THR n 1 91 LEU n 1 92 GLY n 1 93 ASN n 1 94 VAL n 1 95 ASP n 1 96 VAL n 1 97 THR n 1 98 ILE n 1 99 ILE n 1 100 ALA n 1 101 GLN n 1 102 ALA n 1 103 PRO n 1 104 LYS n 1 105 MSE n 1 106 LEU n 1 107 PRO n 1 108 HIS n 1 109 ILE n 1 110 PRO n 1 111 GLN n 1 112 MSE n 1 113 ARG n 1 114 VAL n 1 115 PHE n 1 116 ILE n 1 117 ALA n 1 118 GLU n 1 119 ASP n 1 120 LEU n 1 121 GLY n 1 122 CYS n 1 123 HIS n 1 124 MSE n 1 125 ASP n 1 126 ASP n 1 127 VAL n 1 128 ASN n 1 129 VAL n 1 130 LYS n 1 131 ALA n 1 132 THR n 1 133 THR n 1 134 THR n 1 135 GLU n 1 136 LYS n 1 137 LEU n 1 138 GLY n 1 139 PHE n 1 140 THR n 1 141 GLY n 1 142 ARG n 1 143 GLY n 1 144 GLU n 1 145 GLY n 1 146 ILE n 1 147 ALA n 1 148 CYS n 1 149 GLU n 1 150 ALA n 1 151 VAL n 1 152 ALA n 1 153 LEU n 1 154 LEU n 1 155 ILE n 1 156 LYS n 1 157 ALA n 1 158 THR n 1 159 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 Escherichia _entity_src_gen.pdbx_gene_src_gene ispF _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 562 _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 Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species 'Escherichia coli' _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 PHIS8 _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.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREA WRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIKATK ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession P62617 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1KNJ _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 159 _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 1KNJ MSE A 1 ? UNP P62617 MET 1 'MODIFIED RESIDUE' 1 1 1 1KNJ MSE A 105 ? UNP P62617 MET 105 'MODIFIED RESIDUE' 105 2 1 1KNJ MSE A 112 ? UNP P62617 MET 112 'MODIFIED RESIDUE' 112 3 1 1KNJ MSE A 124 ? UNP P62617 MET 124 'MODIFIED RESIDUE' 124 4 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 C5P non-polymer . "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CDI non-polymer . '2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE' ? 'C5 H12 O9 P2' 278.091 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 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 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 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.entry_id 1KNJ _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_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 294 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '(NH4)2SO4, PEG 400, NaI, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 ? ? 1 1,2 ? ? 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2001-03-26 _diffrn_detector.details mirrors # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'HORIZONTALLY FOCUSED BY SAGITTAL CURVED 2nd CRYSTAL' MAD x-ray 2 1 M 'SAGITALLY FOCUSED Ge(220)' 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9795 1.0 2 0.9800 1.0 3 0.9724 1.0 4 0.9340 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'ESRF BEAMLINE BM30A' ESRF BM30A ? '0.9795, 0.9800, 0.9724' 2 SYNCHROTRON 'ESRF BEAMLINE ID14-1' ESRF ID14-1 ? 0.9340 # _reflns.entry_id 1KNJ _reflns.observed_criterion_sigma_I 1 _reflns.observed_criterion_sigma_F 1 _reflns.d_resolution_low 99.0 _reflns.d_resolution_high 2.7 _reflns.number_obs 11923 _reflns.number_all 11923 _reflns.percent_possible_obs 99.3 _reflns.pdbx_Rmerge_I_obs 0.0400000 _reflns.pdbx_Rsym_value 0.0660000 _reflns.pdbx_netI_over_sigmaI 19 _reflns.B_iso_Wilson_estimate 92.0 _reflns.pdbx_redundancy 4.1 _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_ordinal 1 _reflns.pdbx_diffrn_id 1,2 # _reflns_shell.d_res_high 2.80 _reflns_shell.d_res_low 2.87 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.6600000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 482.0 _reflns_shell.pdbx_redundancy 4.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1579 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1,2 # _refine.entry_id 1KNJ _refine.ls_number_reflns_obs 11262 _refine.ls_number_reflns_all 12817 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF 1949090.32 _refine.pdbx_data_cutoff_low_absF .000000 _refine.ls_d_res_low 14.71 _refine.ls_d_res_high 2.80 _refine.ls_percent_reflns_obs 87.9 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all 0.2860000 _refine.ls_R_factor_R_work 0.2410000 _refine.ls_R_factor_R_free 0.2500000 _refine.ls_R_factor_R_free_error .010 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 577 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 62.6 _refine.aniso_B[1][1] .00 _refine.aniso_B[2][2] .00 _refine.aniso_B[3][3] .00 _refine.aniso_B[1][2] .00 _refine.aniso_B[1][3] .00 _refine.aniso_B[2][3] .00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol .333926 _refine.solvent_model_param_bsol 41.9833 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1KNJ _refine_analyze.Luzzati_coordinate_error_obs .37 _refine_analyze.Luzzati_sigma_a_obs .46 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free .39 _refine_analyze.Luzzati_sigma_a_free .38 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1166 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 38 _refine_hist.number_atoms_solvent 22 _refine_hist.number_atoms_total 1226 _refine_hist.d_res_high 2.80 _refine_hist.d_res_low 14.71 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d .010 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.8 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 23.6 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.52 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.80 _refine_ls_shell.d_res_low 2.98 _refine_ls_shell.number_reflns_R_work 1495 _refine_ls_shell.R_factor_R_work 0.3340000 _refine_ls_shell.percent_reflns_obs 75.1 _refine_ls_shell.R_factor_R_free 0.3700000 _refine_ls_shell.R_factor_R_free_error .038 _refine_ls_shell.percent_reflns_R_free 4.8 _refine_ls_shell.number_reflns_R_free 76 _refine_ls_shell.number_reflns_obs 1495 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' 3 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' 4 LIGAND.PARAM LIGAND.TOP 'X-RAY DIFFRACTION' # _struct.entry_id 1KNJ _struct.title ;Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+ ; _struct.pdbx_descriptor '2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1KNJ _struct_keywords.pdbx_keywords 'METAL BINDING PROTEIN' _struct_keywords.text ;isoprenoids, deoxyxylulose/methyl-erythritol-phosphate pathway, cyclodiphosphate, MEP, YgbB, ispF, MECDP, 2-C-methyl-D-erythritol-2, 4-cyclodiphosphate synthase, METAL BINDING PROTEIN ; # 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 ? # _struct_biol.id 1 _struct_biol.details ;The biological assembly is a homotrimer generated from the monomer in the asymmetric unit by the operations: z,x,y and y,z,x ; _struct_biol.pdbx_parent_biol_id ? # 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 38 ? ALA A 52 ? ASP A 38 ALA A 52 1 ? 15 HELX_P HELX_P2 2 ASP A 56 ? PHE A 61 ? ASP A 56 PHE A 61 5 ? 6 HELX_P HELX_P3 3 ASP A 72 ? LYS A 87 ? ASP A 72 LYS A 87 1 ? 16 HELX_P HELX_P4 4 HIS A 108 ? LEU A 120 ? HIS A 108 LEU A 120 1 ? 13 HELX_P HELX_P5 5 HIS A 123 ? ASP A 125 ? HIS A 123 ASP A 125 5 ? 3 HELX_P HELX_P6 6 LEU A 137 ? ARG A 142 ? 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 covale1 covale ? ? A MSE 1 C ? ? ? 1_555 A ARG 2 N ? ? A MSE 1 A ARG 2 1_555 ? ? ? ? ? ? ? 1.330 ? covale2 covale ? ? A LYS 104 C ? ? ? 1_555 A MSE 105 N ? ? A LYS 104 A MSE 105 1_555 ? ? ? ? ? ? ? 1.328 ? covale3 covale ? ? A MSE 105 C ? ? ? 1_555 A LEU 106 N ? ? A MSE 105 A LEU 106 1_555 ? ? ? ? ? ? ? 1.329 ? covale4 covale ? ? A GLN 111 C ? ? ? 1_555 A MSE 112 N ? ? A GLN 111 A MSE 112 1_555 ? ? ? ? ? ? ? 1.339 ? covale5 covale ? ? A MSE 112 C ? ? ? 1_555 A ARG 113 N ? ? A MSE 112 A ARG 113 1_555 ? ? ? ? ? ? ? 1.327 ? covale6 covale ? ? A HIS 123 C ? ? ? 1_555 A MSE 124 N ? ? A HIS 123 A MSE 124 1_555 ? ? ? ? ? ? ? 1.323 ? covale7 covale ? ? A MSE 124 C ? ? ? 1_555 A ASP 125 N ? ? A MSE 124 A ASP 125 1_555 ? ? ? ? ? ? ? 1.328 ? metalc1 metalc ? ? A ASP 8 OD1 ? ? ? 1_555 B MN . MN ? ? A ASP 8 A MN 401 1_555 ? ? ? ? ? ? ? 2.487 ? metalc2 metalc ? ? A ASP 8 OD2 ? ? ? 1_555 B MN . MN ? ? A ASP 8 A MN 401 1_555 ? ? ? ? ? ? ? 2.298 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id ALA _struct_mon_prot_cis.label_seq_id 102 _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 ALA _struct_mon_prot_cis.auth_seq_id 102 _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_2 103 _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_2 103 _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 -0.66 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? 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 ? 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 ARG A 2 ? ALA A 11 ? ARG A 2 ALA A 11 A 2 GLY A 145 ? ILE A 155 ? GLY A 145 ILE A 155 A 3 THR A 90 ? ILE A 99 ? THR A 90 ILE A 99 A 4 VAL A 127 ? THR A 132 ? VAL A 127 THR A 132 B 1 ILE A 18 ? ILE A 20 ? ILE A 18 ILE A 20 B 2 VAL A 23 ? ILE A 25 ? 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 N GLY A 6 ? N GLY A 6 O ALA A 150 ? O ALA A 150 A 2 3 O ALA A 147 ? O ALA A 147 N ILE A 99 ? N ILE A 99 A 3 4 N VAL A 94 ? N VAL A 94 O ASN A 128 ? O ASN A 128 B 1 2 N ILE A 18 ? N ILE A 18 O ILE A 25 ? 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 MN A 401' AC2 Software ? ? ? ? 12 'BINDING SITE FOR RESIDUE C5P A 201' AC3 Software ? ? ? ? 11 'BINDING SITE FOR RESIDUE CDI 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 4 ASP A 8 ? ASP A 8 . ? 1_555 ? 2 AC1 4 HIS A 10 ? HIS A 10 . ? 1_555 ? 3 AC1 4 HIS A 42 ? HIS A 42 . ? 1_555 ? 4 AC1 4 CDI D . ? CDI A 301 . ? 5_555 ? 5 AC2 12 ASP A 56 ? ASP A 56 . ? 9_555 ? 6 AC2 12 GLY A 58 ? GLY A 58 . ? 9_555 ? 7 AC2 12 ALA A 100 ? ALA A 100 . ? 1_555 ? 8 AC2 12 PRO A 103 ? PRO A 103 . ? 1_555 ? 9 AC2 12 LYS A 104 ? LYS A 104 . ? 1_555 ? 10 AC2 12 MSE A 105 ? MSE A 105 . ? 1_555 ? 11 AC2 12 LEU A 106 ? LEU A 106 . ? 1_555 ? 12 AC2 12 ALA A 131 ? ALA A 131 . ? 1_555 ? 13 AC2 12 THR A 132 ? THR A 132 . ? 1_555 ? 14 AC2 12 THR A 133 ? THR A 133 . ? 1_555 ? 15 AC2 12 GLU A 135 ? GLU A 135 . ? 1_555 ? 16 AC2 12 CDI D . ? CDI A 301 . ? 1_555 ? 17 AC3 11 ASP A 8 ? ASP A 8 . ? 9_555 ? 18 AC3 11 HIS A 10 ? HIS A 10 . ? 9_555 ? 19 AC3 11 ALA A 33 ? ALA A 33 . ? 9_555 ? 20 AC3 11 HIS A 34 ? HIS A 34 . ? 9_555 ? 21 AC3 11 SER A 35 ? SER A 35 . ? 9_555 ? 22 AC3 11 HIS A 42 ? HIS A 42 . ? 9_555 ? 23 AC3 11 ILE A 57 ? ILE A 57 . ? 9_555 ? 24 AC3 11 PRO A 62 ? PRO A 62 . ? 9_555 ? 25 AC3 11 C5P C . ? C5P A 201 . ? 1_555 ? 26 AC3 11 MN B . ? MN A 401 . ? 9_555 ? 27 AC3 11 HOH E . ? HOH A 422 . ? 1_555 ? # _database_PDB_matrix.entry_id 1KNJ _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] .000000 _database_PDB_matrix.origx[1][3] .000000 _database_PDB_matrix.origx[2][1] .000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] .000000 _database_PDB_matrix.origx[3][1] .000000 _database_PDB_matrix.origx[3][2] .000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] .00000 _database_PDB_matrix.origx_vector[2] .00000 _database_PDB_matrix.origx_vector[3] .00000 # _atom_sites.entry_id 1KNJ _atom_sites.fract_transf_matrix[1][1] .006932 _atom_sites.fract_transf_matrix[1][2] .000000 _atom_sites.fract_transf_matrix[1][3] .000000 _atom_sites.fract_transf_matrix[2][1] .000000 _atom_sites.fract_transf_matrix[2][2] .006932 _atom_sites.fract_transf_matrix[2][3] .000000 _atom_sites.fract_transf_matrix[3][1] .000000 _atom_sites.fract_transf_matrix[3][2] .000000 _atom_sites.fract_transf_matrix[3][3] .006932 _atom_sites.fract_transf_vector[1] .00000 _atom_sites.fract_transf_vector[2] .00000 _atom_sites.fract_transf_vector[3] .00000 # loop_ _atom_type.symbol C MN N O P S 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 1 MSE MSE A . n A 1 2 ARG 2 2 2 ARG ARG A . n A 1 3 ILE 3 3 3 ILE ILE A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 HIS 5 5 5 HIS HIS A . n A 1 6 GLY 6 6 6 GLY GLY A . n A 1 7 PHE 7 7 7 PHE PHE A . n A 1 8 ASP 8 8 8 ASP ASP A . n A 1 9 VAL 9 9 9 VAL VAL A . n A 1 10 HIS 10 10 10 HIS HIS A . n A 1 11 ALA 11 11 11 ALA ALA A . n A 1 12 PHE 12 12 12 PHE PHE A . n A 1 13 GLY 13 13 13 GLY GLY A . n A 1 14 GLY 14 14 14 GLY GLY A . n A 1 15 GLU 15 15 15 GLU GLU A . n A 1 16 GLY 16 16 16 GLY GLY A . n A 1 17 PRO 17 17 17 PRO PRO A . n A 1 18 ILE 18 18 18 ILE ILE A . n A 1 19 ILE 19 19 19 ILE ILE A . n A 1 20 ILE 20 20 20 ILE ILE A . n A 1 21 GLY 21 21 21 GLY GLY A . n A 1 22 GLY 22 22 22 GLY GLY A . n A 1 23 VAL 23 23 23 VAL VAL A . n A 1 24 ARG 24 24 24 ARG ARG A . n A 1 25 ILE 25 25 25 ILE ILE A . n A 1 26 PRO 26 26 26 PRO PRO A . n A 1 27 TYR 27 27 27 TYR TYR A . n A 1 28 GLU 28 28 28 GLU GLU A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 GLY 30 30 30 GLY GLY A . n A 1 31 LEU 31 31 31 LEU LEU A . n A 1 32 LEU 32 32 32 LEU LEU A . n A 1 33 ALA 33 33 33 ALA ALA A . n A 1 34 HIS 34 34 34 HIS HIS A . n A 1 35 SER 35 35 35 SER SER A . n A 1 36 ASP 36 36 36 ASP ASP A . n A 1 37 GLY 37 37 37 GLY GLY A . n A 1 38 ASP 38 38 38 ASP ASP A . n A 1 39 VAL 39 39 39 VAL VAL A . n A 1 40 ALA 40 40 40 ALA ALA A . n A 1 41 LEU 41 41 41 LEU LEU A . n A 1 42 HIS 42 42 42 HIS HIS A . n A 1 43 ALA 43 43 43 ALA ALA A . n A 1 44 LEU 44 44 44 LEU LEU A . n A 1 45 THR 45 45 45 THR THR A . n A 1 46 ASP 46 46 46 ASP ASP A . n A 1 47 ALA 47 47 47 ALA ALA A . n A 1 48 LEU 48 48 48 LEU LEU A . n A 1 49 LEU 49 49 49 LEU LEU A . n A 1 50 GLY 50 50 50 GLY GLY A . n A 1 51 ALA 51 51 51 ALA ALA A . n A 1 52 ALA 52 52 52 ALA ALA A . n A 1 53 ALA 53 53 53 ALA ALA A . n A 1 54 LEU 54 54 54 LEU LEU A . n A 1 55 GLY 55 55 55 GLY GLY A . n A 1 56 ASP 56 56 56 ASP ASP A . n A 1 57 ILE 57 57 57 ILE ILE A . n A 1 58 GLY 58 58 58 GLY GLY A . n A 1 59 LYS 59 59 59 LYS LYS A . n A 1 60 LEU 60 60 60 LEU LEU A . n A 1 61 PHE 61 61 61 PHE PHE A . n A 1 62 PRO 62 62 62 PRO PRO A . n A 1 63 ASP 63 63 63 ASP ASP A . n A 1 64 THR 64 64 64 THR THR A . n A 1 65 ASP 65 65 65 ASP ASP A . n A 1 66 PRO 66 66 66 PRO PRO A . n A 1 67 ALA 67 67 67 ALA ALA A . n A 1 68 PHE 68 68 68 PHE PHE A . n A 1 69 LYS 69 69 69 LYS LYS A . n A 1 70 GLY 70 70 70 GLY GLY A . n A 1 71 ALA 71 71 71 ALA ALA A . n A 1 72 ASP 72 72 72 ASP ASP A . n A 1 73 SER 73 73 73 SER SER A . n A 1 74 ARG 74 74 74 ARG ARG A . n A 1 75 GLU 75 75 75 GLU GLU A . n A 1 76 LEU 76 76 76 LEU LEU A . n A 1 77 LEU 77 77 77 LEU LEU A . n A 1 78 ARG 78 78 78 ARG ARG A . n A 1 79 GLU 79 79 79 GLU GLU A . n A 1 80 ALA 80 80 80 ALA ALA A . n A 1 81 TRP 81 81 81 TRP TRP A . n A 1 82 ARG 82 82 82 ARG ARG A . n A 1 83 ARG 83 83 83 ARG ARG A . n A 1 84 ILE 84 84 84 ILE ILE A . n A 1 85 GLN 85 85 85 GLN GLN A . n A 1 86 ALA 86 86 86 ALA ALA A . n A 1 87 LYS 87 87 87 LYS LYS A . n A 1 88 GLY 88 88 88 GLY GLY A . n A 1 89 TYR 89 89 89 TYR TYR A . n A 1 90 THR 90 90 90 THR THR A . n A 1 91 LEU 91 91 91 LEU LEU A . n A 1 92 GLY 92 92 92 GLY GLY A . n A 1 93 ASN 93 93 93 ASN ASN A . n A 1 94 VAL 94 94 94 VAL VAL A . n A 1 95 ASP 95 95 95 ASP ASP A . n A 1 96 VAL 96 96 96 VAL VAL A . n A 1 97 THR 97 97 97 THR THR A . n A 1 98 ILE 98 98 98 ILE ILE A . n A 1 99 ILE 99 99 99 ILE ILE A . n A 1 100 ALA 100 100 100 ALA ALA A . n A 1 101 GLN 101 101 101 GLN GLN A . n A 1 102 ALA 102 102 102 ALA ALA A . n A 1 103 PRO 103 103 103 PRO PRO A . n A 1 104 LYS 104 104 104 LYS LYS A . n A 1 105 MSE 105 105 105 MSE MSE A . n A 1 106 LEU 106 106 106 LEU LEU A . n A 1 107 PRO 107 107 107 PRO PRO A . n A 1 108 HIS 108 108 108 HIS HIS A . n A 1 109 ILE 109 109 109 ILE ILE A . n A 1 110 PRO 110 110 110 PRO PRO A . n A 1 111 GLN 111 111 111 GLN GLN A . n A 1 112 MSE 112 112 112 MSE MSE A . n A 1 113 ARG 113 113 113 ARG ARG A . n A 1 114 VAL 114 114 114 VAL VAL A . n A 1 115 PHE 115 115 115 PHE PHE A . n A 1 116 ILE 116 116 116 ILE ILE A . n A 1 117 ALA 117 117 117 ALA ALA A . n A 1 118 GLU 118 118 118 GLU GLU A . n A 1 119 ASP 119 119 119 ASP ASP A . n A 1 120 LEU 120 120 120 LEU LEU A . n A 1 121 GLY 121 121 121 GLY GLY A . n A 1 122 CYS 122 122 122 CYS CYS A . n A 1 123 HIS 123 123 123 HIS HIS A . n A 1 124 MSE 124 124 124 MSE MSE A . n A 1 125 ASP 125 125 125 ASP ASP A . n A 1 126 ASP 126 126 126 ASP ASP A . n A 1 127 VAL 127 127 127 VAL VAL A . n A 1 128 ASN 128 128 128 ASN ASN A . n A 1 129 VAL 129 129 129 VAL VAL A . n A 1 130 LYS 130 130 130 LYS LYS A . n A 1 131 ALA 131 131 131 ALA ALA A . n A 1 132 THR 132 132 132 THR THR A . n A 1 133 THR 133 133 133 THR THR A . n A 1 134 THR 134 134 134 THR THR A . n A 1 135 GLU 135 135 135 GLU GLU A . n A 1 136 LYS 136 136 136 LYS LYS A . n A 1 137 LEU 137 137 137 LEU LEU A . n A 1 138 GLY 138 138 138 GLY GLY A . n A 1 139 PHE 139 139 139 PHE PHE A . n A 1 140 THR 140 140 140 THR THR A . n A 1 141 GLY 141 141 141 GLY GLY A . n A 1 142 ARG 142 142 142 ARG ARG A . n A 1 143 GLY 143 143 143 GLY GLY A . n A 1 144 GLU 144 144 144 GLU GLU A . n A 1 145 GLY 145 145 145 GLY GLY A . n A 1 146 ILE 146 146 146 ILE ILE A . n A 1 147 ALA 147 147 147 ALA ALA A . n A 1 148 CYS 148 148 148 CYS CYS A . n A 1 149 GLU 149 149 149 GLU GLU A . n A 1 150 ALA 150 150 150 ALA ALA A . n A 1 151 VAL 151 151 151 VAL VAL A . n A 1 152 ALA 152 152 152 ALA ALA A . n A 1 153 LEU 153 153 153 LEU LEU A . n A 1 154 LEU 154 154 154 LEU LEU A . n A 1 155 ILE 155 155 155 ILE ILE A . n A 1 156 LYS 156 156 156 LYS LYS A . n A 1 157 ALA 157 157 ? ? ? A . n A 1 158 THR 158 158 ? ? ? A . n A 1 159 LYS 159 159 ? ? ? A . n # 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 1 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 105 A MSE 105 ? MET SELENOMETHIONINE 3 A MSE 112 A MSE 112 ? MET SELENOMETHIONINE 4 A MSE 124 A MSE 124 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA,PQS _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 # 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)' 9660 ? 1 MORE -46 ? 1 'SSA (A^2)' 16120 ? # 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 HOH 403 ? E HOH . 2 1 A HOH 413 ? E HOH . # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id OD1 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id ASP _pdbx_struct_conn_angle.ptnr1_label_seq_id 8 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id ASP _pdbx_struct_conn_angle.ptnr1_auth_seq_id 8 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id MN _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id B _pdbx_struct_conn_angle.ptnr2_label_comp_id MN _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id MN _pdbx_struct_conn_angle.ptnr2_auth_seq_id 401 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id OD2 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id A _pdbx_struct_conn_angle.ptnr3_label_comp_id ASP _pdbx_struct_conn_angle.ptnr3_label_seq_id 8 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id ASP _pdbx_struct_conn_angle.ptnr3_auth_seq_id 8 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 55.0 _pdbx_struct_conn_angle.value_esd ? # 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 2002-06-18 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Derived calculations' 3 3 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement . ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing . ? 4 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 C A GLY 16 ? ? N A PRO 17 ? ? CA A PRO 17 ? ? 131.17 119.30 11.87 1.50 Y 2 1 C A PHE 61 ? ? N A PRO 62 ? ? CA A PRO 62 ? ? 140.27 119.30 20.97 1.50 Y 3 1 C A PHE 61 ? ? N A PRO 62 ? ? CD A PRO 62 ? ? 103.01 128.40 -25.39 2.10 Y # 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 8 ? ? -170.55 145.07 2 1 GLU A 15 ? ? -65.48 -130.65 3 1 PRO A 17 ? ? -20.50 139.88 4 1 TYR A 27 ? ? -172.94 140.67 5 1 ASP A 56 ? ? 33.54 169.16 6 1 PHE A 61 ? ? 64.00 158.96 7 1 PRO A 62 ? ? -142.13 35.26 8 1 THR A 64 ? ? 38.74 57.53 9 1 PRO A 66 ? ? -14.03 86.25 10 1 ALA A 67 ? ? 172.42 -61.07 11 1 LYS A 69 ? ? 153.84 119.68 12 1 LYS A 87 ? ? -80.53 31.14 # 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 ALA 157 ? A ALA 157 2 1 Y 1 A THR 158 ? A THR 158 3 1 Y 1 A LYS 159 ? A LYS 159 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MANGANESE (II) ION' MN 3 "CYTIDINE-5'-MONOPHOSPHATE" C5P 4 '2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE' CDI 5 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 MN 1 401 1 MN MN A . C 3 C5P 1 201 1 C5P C5P A . D 4 CDI 1 301 1 CDI PBB A . E 5 HOH 1 402 1 HOH HOH A . E 5 HOH 2 403 2 HOH HOH A . E 5 HOH 3 404 3 HOH HOH A . E 5 HOH 4 405 4 HOH HOH A . E 5 HOH 5 406 5 HOH HOH A . E 5 HOH 6 407 6 HOH HOH A . E 5 HOH 7 408 7 HOH HOH A . E 5 HOH 8 409 8 HOH HOH A . E 5 HOH 9 410 9 HOH HOH A . E 5 HOH 10 411 10 HOH HOH A . E 5 HOH 11 412 11 HOH HOH A . E 5 HOH 12 413 12 HOH HOH A . E 5 HOH 13 414 13 HOH HOH A . E 5 HOH 14 415 14 HOH HOH A . E 5 HOH 15 416 15 HOH HOH A . E 5 HOH 16 417 16 HOH HOH A . E 5 HOH 17 418 17 HOH HOH A . E 5 HOH 18 419 18 HOH HOH A . E 5 HOH 19 420 19 HOH HOH A . E 5 HOH 20 421 20 HOH HOH A . E 5 HOH 21 422 21 HOH HOH A . E 5 HOH 22 423 22 HOH HOH A . #