data_4RRI # _entry.id 4RRI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4RRI RCSB RCSB087707 WWPDB D_1000087707 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4RR6 . unspecified PDB 4RR7 . unspecified PDB 4RR8 . unspecified PDB 4RR9 . unspecified PDB 4RRA . unspecified PDB 4RRB . unspecified PDB 4RRC . unspecified PDB 4RRD . unspecified PDB 4RRF . unspecified PDB 4RRG . unspecified PDB 4RRH . unspecified PDB 4RRJ . unspecified PDB 4RRK . unspecified PDB 4RRL . unspecified PDB 4RRM . unspecified PDB 4RRQ . unspecified PDB 4RRR . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4RRI _pdbx_database_status.recvd_initial_deposition_date 2014-11-06 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ahmad, S.' 1 'Muthukumar, S.' 2 'Sankaranarayanan, R.' 3 # _citation.id primary _citation.title 'Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.' _citation.journal_abbrev 'Nat Commun' _citation.journal_volume 6 _citation.page_first 7552 _citation.page_last 7552 _citation.year 2015 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 2041-1723 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 26113036 _citation.pdbx_database_id_DOI 10.1038/ncomms8552 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Ahmad, S.' 1 primary 'Muthukumar, S.' 2 primary 'Kuncha, S.K.' 3 primary 'Routh, S.B.' 4 primary 'Yerabham, A.S.' 5 primary 'Hussain, T.' 6 primary 'Kamarthapu, V.' 7 primary 'Kruparani, S.P.' 8 primary 'Sankaranarayanan, R.' 9 # _cell.entry_id 4RRI _cell.length_a 47.119 _cell.length_b 47.119 _cell.length_c 113.124 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 4RRI _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _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 'Probable threonine--tRNA ligase 2' 15137.429 1 6.1.1.3 K116M 'UNP residues 1-136' ? 2 non-polymer syn "3'-deoxy-3'-(L-threonylamino)adenosine" 367.360 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 100 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Threonyl-tRNA synthetase 2, ThrRS 2' # _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 ;MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQTVMYAASDIASHSSRLKVTTVILYPYAHLSS RLAKPMAAHKRLIELEGALRTKFPGHVHRAPFGWYMSFSIACKGHPLAELSRSFTE ; _entity_poly.pdbx_seq_one_letter_code_can ;MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQTVMYAASDIASHSSRLKVTTVILYPYAHLSS RLAKPMAAHKRLIELEGALRTKFPGHVHRAPFGWYMSFSIACKGHPLAELSRSFTE ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 ARG n 1 3 LEU n 1 4 LEU n 1 5 TYR n 1 6 LEU n 1 7 HIS n 1 8 ALA n 1 9 ASP n 1 10 ARG n 1 11 PHE n 1 12 GLU n 1 13 TYR n 1 14 LYS n 1 15 THR n 1 16 VAL n 1 17 LYS n 1 18 PRO n 1 19 ALA n 1 20 LEU n 1 21 LYS n 1 22 ASN n 1 23 PRO n 1 24 PRO n 1 25 ASP n 1 26 PRO n 1 27 PRO n 1 28 GLY n 1 29 GLU n 1 30 ALA n 1 31 SER n 1 32 PHE n 1 33 GLY n 1 34 GLU n 1 35 ALA n 1 36 LEU n 1 37 VAL n 1 38 VAL n 1 39 PHE n 1 40 THR n 1 41 THR n 1 42 VAL n 1 43 GLU n 1 44 ASP n 1 45 GLY n 1 46 ASP n 1 47 GLY n 1 48 PRO n 1 49 GLN n 1 50 THR n 1 51 VAL n 1 52 MET n 1 53 TYR n 1 54 ALA n 1 55 ALA n 1 56 SER n 1 57 ASP n 1 58 ILE n 1 59 ALA n 1 60 SER n 1 61 HIS n 1 62 SER n 1 63 SER n 1 64 ARG n 1 65 LEU n 1 66 LYS n 1 67 VAL n 1 68 THR n 1 69 THR n 1 70 VAL n 1 71 ILE n 1 72 LEU n 1 73 TYR n 1 74 PRO n 1 75 TYR n 1 76 ALA n 1 77 HIS n 1 78 LEU n 1 79 SER n 1 80 SER n 1 81 ARG n 1 82 LEU n 1 83 ALA n 1 84 LYS n 1 85 PRO n 1 86 MET n 1 87 ALA n 1 88 ALA n 1 89 HIS n 1 90 LYS n 1 91 ARG n 1 92 LEU n 1 93 ILE n 1 94 GLU n 1 95 LEU n 1 96 GLU n 1 97 GLY n 1 98 ALA n 1 99 LEU n 1 100 ARG n 1 101 THR n 1 102 LYS n 1 103 PHE n 1 104 PRO n 1 105 GLY n 1 106 HIS n 1 107 VAL n 1 108 HIS n 1 109 ARG n 1 110 ALA n 1 111 PRO n 1 112 PHE n 1 113 GLY n 1 114 TRP n 1 115 TYR n 1 116 MET n 1 117 SER n 1 118 PHE n 1 119 SER n 1 120 ILE n 1 121 ALA n 1 122 CYS n 1 123 LYS n 1 124 GLY n 1 125 HIS n 1 126 PRO n 1 127 LEU n 1 128 ALA n 1 129 GLU n 1 130 LEU n 1 131 SER n 1 132 ARG n 1 133 SER n 1 134 PHE n 1 135 THR n 1 136 GLU 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 'thrS2, APE_0117.1' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1' _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 'Aeropyrum pernix' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 272557 _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 SYT2_AERPE _struct_ref.pdbx_db_accession Q9YFY3 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQTVMYAASDIASHSSRLKVTTVILYPYAHLSS RLAKPMAAHKRLIELEGALRTKFPGHVHRAPFGWYKSFSIACKGHPLAELSRSFTE ; _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 4RRI _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 136 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9YFY3 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 136 _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 136 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4RRI _struct_ref_seq_dif.mon_id MET _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 116 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q9YFY3 _struct_ref_seq_dif.db_mon_id LYS _struct_ref_seq_dif.pdbx_seq_db_seq_num 116 _struct_ref_seq_dif.details 'ENGINEERED MUTATION' _struct_ref_seq_dif.pdbx_auth_seq_num 116 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 A3T non-polymer . "3'-deoxy-3'-(L-threonylamino)adenosine" ? 'C14 H21 N7 O5' 367.360 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 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 4RRI _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.07 _exptl_crystal.density_percent_sol 40.69 _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 8.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '0.1M Tris HCl pH 8.5, 0.2M MgCl2, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV++' _diffrn_detector.pdbx_collection_date 2012-11-15 _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 Mirrors _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU FR-E+ SUPERBRIGHT' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4RRI _reflns.observed_criterion_sigma_I 2 _reflns.observed_criterion_sigma_F 2 _reflns.d_resolution_low 25 _reflns.d_resolution_high 1.50 _reflns.number_obs 19968 _reflns.number_all 20109 _reflns.percent_possible_obs 99.3 _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 ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4RRI _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 19968 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 25.00 _refine.ls_d_res_high 1.50 _refine.ls_percent_reflns_obs 99.3 _refine.ls_R_factor_obs 0.195 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.191 _refine.ls_R_factor_R_free 0.262 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.100 _refine.ls_number_reflns_R_free 1083 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.940 _refine.B_iso_mean 22.40 _refine.aniso_B[1][1] 0.02000 _refine.aniso_B[2][2] 0.02000 _refine.aniso_B[3][3] -0.04000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.105 _refine.pdbx_overall_ESU_R_Free 0.098 _refine.overall_SU_ML 0.076 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 4.650 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1067 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 27 _refine_hist.number_atoms_solvent 100 _refine_hist.number_atoms_total 1194 _refine_hist.d_res_high 1.50 _refine_hist.d_res_low 25.00 # 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 r_bond_refined_d 0.018 0.020 ? 1123 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.943 1.997 ? 1529 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.421 5.000 ? 135 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 43.001 21.591 ? 44 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 14.208 15.000 ? 173 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 10.671 15.000 ? 8 'X-RAY DIFFRACTION' ? r_chiral_restr 0.120 0.200 ? 168 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.012 0.022 ? 853 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 6.088 3.000 ? 1123 'X-RAY DIFFRACTION' ? r_sphericity_free 30.342 5.000 ? 34 'X-RAY DIFFRACTION' ? r_sphericity_bonded 16.283 5.000 ? 1157 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.50 _refine_ls_shell.d_res_low 1.54 _refine_ls_shell.number_reflns_R_work 1237 _refine_ls_shell.R_factor_R_work 0.4020 _refine_ls_shell.percent_reflns_obs 96.17 _refine_ls_shell.R_factor_R_free 0.5150 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 70 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 4RRI _struct.title 'K116M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA' _struct.pdbx_descriptor 'Probable threonine--tRNA ligase 2 (E.C.6.1.1.3)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4RRI _struct_keywords.pdbx_keywords LIGASE _struct_keywords.text 'DTD-like fold, Proofreading, LIGASE' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLY A 47 ? LYS A 66 ? GLY A 47 LYS A 66 1 ? 20 HELX_P HELX_P2 2 LYS A 84 ? ARG A 100 ? LYS A 84 ARG A 100 1 ? 17 # _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 ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 502 A HOH 606 1_555 ? ? ? ? ? ? ? 1.962 ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 502 A HOH 662 1_555 ? ? ? ? ? ? ? 2.095 ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 502 A HOH 622 1_555 ? ? ? ? ? ? ? 2.188 ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 502 A HOH 693 1_555 ? ? ? ? ? ? ? 2.343 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 3 ? B ? 5 ? # 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 B 1 2 ? parallel B 2 3 ? parallel B 3 4 ? anti-parallel B 4 5 ? 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 GLU A 29 ? PHE A 32 ? GLU A 29 PHE A 32 A 2 ARG A 2 ? PRO A 18 ? ARG A 2 PRO A 18 A 3 TRP A 114 ? CYS A 122 ? TRP A 114 CYS A 122 B 1 HIS A 106 ? ARG A 109 ? HIS A 106 ARG A 109 B 2 THR A 69 ? PRO A 74 ? THR A 69 PRO A 74 B 3 ALA A 35 ? THR A 41 ? ALA A 35 THR A 41 B 4 ARG A 2 ? PRO A 18 ? ARG A 2 PRO A 18 B 5 GLU A 129 ? SER A 133 ? GLU A 129 SER A 133 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O PHE A 32 ? O PHE A 32 N PHE A 11 ? N PHE A 11 A 2 3 N VAL A 16 ? N VAL A 16 O TYR A 115 ? O TYR A 115 B 1 2 O HIS A 108 ? O HIS A 108 N LEU A 72 ? N LEU A 72 B 2 3 O ILE A 71 ? O ILE A 71 N LEU A 36 ? N LEU A 36 B 3 4 O VAL A 37 ? O VAL A 37 N LEU A 6 ? N LEU A 6 B 4 5 N TYR A 5 ? N TYR A 5 O LEU A 130 ? O LEU A 130 # 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 ? ? ? ? 20 'BINDING SITE FOR RESIDUE A3T A 501' AC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE MG A 502' # 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 20 ALA A 19 ? ALA A 19 . ? 1_555 ? 2 AC1 20 THR A 40 ? THR A 40 . ? 1_555 ? 3 AC1 20 VAL A 42 ? VAL A 42 . ? 1_555 ? 4 AC1 20 PRO A 74 ? PRO A 74 . ? 1_555 ? 5 AC1 20 TYR A 75 ? TYR A 75 . ? 1_555 ? 6 AC1 20 ALA A 76 ? ALA A 76 . ? 1_555 ? 7 AC1 20 LEU A 82 ? LEU A 82 . ? 1_555 ? 8 AC1 20 ALA A 83 ? ALA A 83 . ? 1_555 ? 9 AC1 20 ALA A 88 ? ALA A 88 . ? 1_555 ? 10 AC1 20 PHE A 112 ? PHE A 112 . ? 1_555 ? 11 AC1 20 GLY A 113 ? GLY A 113 . ? 1_555 ? 12 AC1 20 TRP A 114 ? TRP A 114 . ? 1_555 ? 13 AC1 20 TYR A 115 ? TYR A 115 . ? 1_555 ? 14 AC1 20 MET A 116 ? MET A 116 . ? 1_555 ? 15 AC1 20 GLU A 129 ? GLU A 129 . ? 8_555 ? 16 AC1 20 HOH D . ? HOH A 605 . ? 1_555 ? 17 AC1 20 HOH D . ? HOH A 640 . ? 1_555 ? 18 AC1 20 HOH D . ? HOH A 642 . ? 1_555 ? 19 AC1 20 HOH D . ? HOH A 643 . ? 1_555 ? 20 AC1 20 HOH D . ? HOH A 659 . ? 1_555 ? 21 AC2 6 HOH D . ? HOH A 606 . ? 1_555 ? 22 AC2 6 HOH D . ? HOH A 622 . ? 1_555 ? 23 AC2 6 HOH D . ? HOH A 623 . ? 8_565 ? 24 AC2 6 HOH D . ? HOH A 636 . ? 8_565 ? 25 AC2 6 HOH D . ? HOH A 662 . ? 1_555 ? 26 AC2 6 HOH D . ? HOH A 693 . ? 1_555 ? # _database_PDB_matrix.entry_id 4RRI _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 4RRI _atom_sites.fract_transf_matrix[1][1] 0.021223 _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] 0.021223 _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] 0.008840 _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 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 MET 1 1 1 MET MET A . n A 1 2 ARG 2 2 2 ARG ARG A . n A 1 3 LEU 3 3 3 LEU LEU A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 TYR 5 5 5 TYR TYR A . n A 1 6 LEU 6 6 6 LEU LEU A . n A 1 7 HIS 7 7 7 HIS HIS A . n A 1 8 ALA 8 8 8 ALA ALA A . n A 1 9 ASP 9 9 9 ASP ASP A . n A 1 10 ARG 10 10 10 ARG ARG A . n A 1 11 PHE 11 11 11 PHE PHE A . n A 1 12 GLU 12 12 12 GLU GLU A . n A 1 13 TYR 13 13 13 TYR TYR A . n A 1 14 LYS 14 14 14 LYS LYS A . n A 1 15 THR 15 15 15 THR THR A . n A 1 16 VAL 16 16 16 VAL VAL A . n A 1 17 LYS 17 17 17 LYS LYS A . n A 1 18 PRO 18 18 18 PRO PRO A . n A 1 19 ALA 19 19 19 ALA ALA A . n A 1 20 LEU 20 20 20 LEU LEU A . n A 1 21 LYS 21 21 21 LYS LYS A . n A 1 22 ASN 22 22 22 ASN ASN A . n A 1 23 PRO 23 23 23 PRO PRO A . n A 1 24 PRO 24 24 24 PRO PRO A . n A 1 25 ASP 25 25 25 ASP ASP A . n A 1 26 PRO 26 26 26 PRO PRO A . n A 1 27 PRO 27 27 27 PRO PRO A . n A 1 28 GLY 28 28 28 GLY GLY A . n A 1 29 GLU 29 29 29 GLU GLU A . n A 1 30 ALA 30 30 30 ALA ALA A . n A 1 31 SER 31 31 31 SER SER A . n A 1 32 PHE 32 32 32 PHE PHE A . n A 1 33 GLY 33 33 33 GLY GLY A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 ALA 35 35 35 ALA ALA A . n A 1 36 LEU 36 36 36 LEU LEU A . n A 1 37 VAL 37 37 37 VAL VAL A . n A 1 38 VAL 38 38 38 VAL VAL A . n A 1 39 PHE 39 39 39 PHE PHE A . n A 1 40 THR 40 40 40 THR THR A . n A 1 41 THR 41 41 41 THR THR A . n A 1 42 VAL 42 42 42 VAL VAL A . n A 1 43 GLU 43 43 43 GLU GLU A . n A 1 44 ASP 44 44 44 ASP ASP A . n A 1 45 GLY 45 45 45 GLY GLY A . n A 1 46 ASP 46 46 46 ASP ASP A . n A 1 47 GLY 47 47 47 GLY GLY A . n A 1 48 PRO 48 48 48 PRO PRO A . n A 1 49 GLN 49 49 49 GLN GLN A . n A 1 50 THR 50 50 50 THR THR A . n A 1 51 VAL 51 51 51 VAL VAL A . n A 1 52 MET 52 52 52 MET MET A . n A 1 53 TYR 53 53 53 TYR TYR A . n A 1 54 ALA 54 54 54 ALA ALA A . n A 1 55 ALA 55 55 55 ALA ALA A . n A 1 56 SER 56 56 56 SER SER A . n A 1 57 ASP 57 57 57 ASP ASP A . n A 1 58 ILE 58 58 58 ILE ILE A . n A 1 59 ALA 59 59 59 ALA ALA A . n A 1 60 SER 60 60 60 SER SER A . n A 1 61 HIS 61 61 61 HIS HIS A . n A 1 62 SER 62 62 62 SER SER A . n A 1 63 SER 63 63 63 SER SER A . n A 1 64 ARG 64 64 64 ARG ARG A . n A 1 65 LEU 65 65 65 LEU LEU A . n A 1 66 LYS 66 66 66 LYS LYS A . n A 1 67 VAL 67 67 67 VAL VAL A . n A 1 68 THR 68 68 68 THR THR A . n A 1 69 THR 69 69 69 THR THR A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 ILE 71 71 71 ILE ILE A . n A 1 72 LEU 72 72 72 LEU LEU A . n A 1 73 TYR 73 73 73 TYR TYR A . n A 1 74 PRO 74 74 74 PRO PRO A . n A 1 75 TYR 75 75 75 TYR TYR A . n A 1 76 ALA 76 76 76 ALA ALA A . n A 1 77 HIS 77 77 77 HIS HIS A . n A 1 78 LEU 78 78 78 LEU LEU A . n A 1 79 SER 79 79 79 SER SER A . n A 1 80 SER 80 80 80 SER SER A . n A 1 81 ARG 81 81 81 ARG ARG A . n A 1 82 LEU 82 82 82 LEU LEU A . n A 1 83 ALA 83 83 83 ALA ALA A . n A 1 84 LYS 84 84 84 LYS LYS A . n A 1 85 PRO 85 85 85 PRO PRO A . n A 1 86 MET 86 86 86 MET MET A . n A 1 87 ALA 87 87 87 ALA ALA A . n A 1 88 ALA 88 88 88 ALA ALA A . n A 1 89 HIS 89 89 89 HIS HIS A . n A 1 90 LYS 90 90 90 LYS LYS A . n A 1 91 ARG 91 91 91 ARG ARG A . n A 1 92 LEU 92 92 92 LEU LEU A . n A 1 93 ILE 93 93 93 ILE ILE A . n A 1 94 GLU 94 94 94 GLU GLU A . n A 1 95 LEU 95 95 95 LEU LEU A . n A 1 96 GLU 96 96 96 GLU GLU A . n A 1 97 GLY 97 97 97 GLY GLY A . n A 1 98 ALA 98 98 98 ALA ALA A . n A 1 99 LEU 99 99 99 LEU LEU A . n A 1 100 ARG 100 100 100 ARG ARG A . n A 1 101 THR 101 101 101 THR THR A . n A 1 102 LYS 102 102 102 LYS LYS A . n A 1 103 PHE 103 103 103 PHE PHE A . n A 1 104 PRO 104 104 104 PRO PRO A . n A 1 105 GLY 105 105 105 GLY GLY A . n A 1 106 HIS 106 106 106 HIS HIS A . n A 1 107 VAL 107 107 107 VAL VAL A . n A 1 108 HIS 108 108 108 HIS HIS A . n A 1 109 ARG 109 109 109 ARG ARG A . n A 1 110 ALA 110 110 110 ALA ALA A . n A 1 111 PRO 111 111 111 PRO PRO A . n A 1 112 PHE 112 112 112 PHE PHE A . n A 1 113 GLY 113 113 113 GLY GLY A . n A 1 114 TRP 114 114 114 TRP TRP A . n A 1 115 TYR 115 115 115 TYR TYR A . n A 1 116 MET 116 116 116 MET MET A . n A 1 117 SER 117 117 117 SER SER A . n A 1 118 PHE 118 118 118 PHE PHE A . n A 1 119 SER 119 119 119 SER SER A . n A 1 120 ILE 120 120 120 ILE ILE A . n A 1 121 ALA 121 121 121 ALA ALA A . n A 1 122 CYS 122 122 122 CYS CYS A . n A 1 123 LYS 123 123 123 LYS LYS A . n A 1 124 GLY 124 124 124 GLY GLY A . n A 1 125 HIS 125 125 125 HIS HIS A . n A 1 126 PRO 126 126 126 PRO PRO A . n A 1 127 LEU 127 127 127 LEU LEU A . n A 1 128 ALA 128 128 128 ALA ALA A . n A 1 129 GLU 129 129 129 GLU GLU A . n A 1 130 LEU 130 130 130 LEU LEU A . n A 1 131 SER 131 131 131 SER SER A . n A 1 132 ARG 132 132 132 ARG ARG A . n A 1 133 SER 133 133 133 SER SER A . n A 1 134 PHE 134 134 134 PHE PHE A . n A 1 135 THR 135 135 135 THR THR A . n A 1 136 GLU 136 136 136 GLU GLU A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 A3T 1 501 501 A3T A3T A . C 3 MG 1 502 1 MG MG A . D 4 HOH 1 601 1 HOH HOH A . D 4 HOH 2 602 2 HOH HOH A . D 4 HOH 3 603 3 HOH HOH A . D 4 HOH 4 604 4 HOH HOH A . D 4 HOH 5 605 5 HOH HOH A . D 4 HOH 6 606 6 HOH HOH A . D 4 HOH 7 607 7 HOH HOH A . D 4 HOH 8 608 8 HOH HOH A . D 4 HOH 9 609 9 HOH HOH A . D 4 HOH 10 610 10 HOH HOH A . D 4 HOH 11 611 11 HOH HOH A . D 4 HOH 12 612 12 HOH HOH A . D 4 HOH 13 613 13 HOH HOH A . D 4 HOH 14 614 14 HOH HOH A . D 4 HOH 15 615 15 HOH HOH A . D 4 HOH 16 616 16 HOH HOH A . D 4 HOH 17 617 17 HOH HOH A . D 4 HOH 18 618 18 HOH HOH A . D 4 HOH 19 619 19 HOH HOH A . D 4 HOH 20 620 20 HOH HOH A . D 4 HOH 21 621 21 HOH HOH A . D 4 HOH 22 622 22 HOH HOH A . D 4 HOH 23 623 23 HOH HOH A . D 4 HOH 24 624 24 HOH HOH A . D 4 HOH 25 625 25 HOH HOH A . D 4 HOH 26 626 26 HOH HOH A . D 4 HOH 27 627 27 HOH HOH A . D 4 HOH 28 628 28 HOH HOH A . D 4 HOH 29 629 29 HOH HOH A . D 4 HOH 30 630 30 HOH HOH A . D 4 HOH 31 631 31 HOH HOH A . D 4 HOH 32 632 32 HOH HOH A . D 4 HOH 33 633 33 HOH HOH A . D 4 HOH 34 634 35 HOH HOH A . D 4 HOH 35 635 36 HOH HOH A . D 4 HOH 36 636 37 HOH HOH A . D 4 HOH 37 637 38 HOH HOH A . D 4 HOH 38 638 39 HOH HOH A . D 4 HOH 39 639 40 HOH HOH A . D 4 HOH 40 640 41 HOH HOH A . D 4 HOH 41 641 42 HOH HOH A . D 4 HOH 42 642 43 HOH HOH A . D 4 HOH 43 643 45 HOH HOH A . D 4 HOH 44 644 46 HOH HOH A . D 4 HOH 45 645 56 HOH HOH A . D 4 HOH 46 646 57 HOH HOH A . D 4 HOH 47 647 58 HOH HOH A . D 4 HOH 48 648 59 HOH HOH A . D 4 HOH 49 649 60 HOH HOH A . D 4 HOH 50 650 61 HOH HOH A . D 4 HOH 51 651 62 HOH HOH A . D 4 HOH 52 652 63 HOH HOH A . D 4 HOH 53 653 64 HOH HOH A . D 4 HOH 54 654 65 HOH HOH A . D 4 HOH 55 655 66 HOH HOH A . D 4 HOH 56 656 67 HOH HOH A . D 4 HOH 57 657 68 HOH HOH A . D 4 HOH 58 658 69 HOH HOH A . D 4 HOH 59 659 70 HOH HOH A . D 4 HOH 60 660 71 HOH HOH A . D 4 HOH 61 661 72 HOH HOH A . D 4 HOH 62 662 73 HOH HOH A . D 4 HOH 63 663 74 HOH HOH A . D 4 HOH 64 664 76 HOH HOH A . D 4 HOH 65 665 77 HOH HOH A . D 4 HOH 66 666 78 HOH HOH A . D 4 HOH 67 667 79 HOH HOH A . D 4 HOH 68 668 80 HOH HOH A . D 4 HOH 69 669 81 HOH HOH A . D 4 HOH 70 670 82 HOH HOH A . D 4 HOH 71 671 83 HOH HOH A . D 4 HOH 72 672 84 HOH HOH A . D 4 HOH 73 673 85 HOH HOH A . D 4 HOH 74 674 86 HOH HOH A . D 4 HOH 75 675 87 HOH HOH A . D 4 HOH 76 676 91 HOH HOH A . D 4 HOH 77 677 92 HOH HOH A . D 4 HOH 78 678 93 HOH HOH A . D 4 HOH 79 679 94 HOH HOH A . D 4 HOH 80 680 95 HOH HOH A . D 4 HOH 81 681 101 HOH HOH A . D 4 HOH 82 682 102 HOH HOH A . D 4 HOH 83 683 103 HOH HOH A . D 4 HOH 84 684 104 HOH HOH A . D 4 HOH 85 685 105 HOH HOH A . D 4 HOH 86 686 106 HOH HOH A . D 4 HOH 87 687 107 HOH HOH A . D 4 HOH 88 688 111 HOH HOH A . D 4 HOH 89 689 112 HOH HOH A . D 4 HOH 90 690 113 HOH HOH A . D 4 HOH 91 691 115 HOH HOH A . D 4 HOH 92 692 116 HOH HOH A . D 4 HOH 93 693 117 HOH HOH A . D 4 HOH 94 694 118 HOH HOH A . D 4 HOH 95 695 119 HOH HOH A . D 4 HOH 96 696 120 HOH HOH A . D 4 HOH 97 697 121 HOH HOH A . D 4 HOH 98 698 122 HOH HOH A . D 4 HOH 99 699 123 HOH HOH A . D 4 HOH 100 700 124 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 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,D # 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)' 2090 ? 1 MORE -5 ? 1 'SSA (A^2)' 11960 ? # 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' 8_555 -y,-x,-z+1/2 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 56.5620000000 # 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 676 ? D HOH . 2 1 A HOH 700 ? D HOH . # 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 O ? D HOH . ? A HOH 606 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O ? D HOH . ? A HOH 662 ? 1_555 91.5 ? 2 O ? D HOH . ? A HOH 606 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O ? D HOH . ? A HOH 622 ? 1_555 89.9 ? 3 O ? D HOH . ? A HOH 662 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O ? D HOH . ? A HOH 622 ? 1_555 177.8 ? 4 O ? D HOH . ? A HOH 606 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O ? D HOH . ? A HOH 693 ? 1_555 87.7 ? 5 O ? D HOH . ? A HOH 662 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O ? D HOH . ? A HOH 693 ? 1_555 95.8 ? 6 O ? D HOH . ? A HOH 622 ? 1_555 MG ? C MG . ? A MG 502 ? 1_555 O ? D HOH . ? A HOH 693 ? 1_555 85.9 ? # 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 2015-07-15 2 'Structure model' 1 1 2017-11-22 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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' Advisory 2 2 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' pdbx_unobs_or_zero_occ_atoms 2 2 'Structure model' software # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_software.classification' 2 2 'Structure model' '_software.name' 3 2 'Structure model' '_software.version' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CrystalClear 'data collection' . ? 1 MOLREP phasing . ? 2 PHASER phasing . ? 3 REFMAC refinement 5.6.0117 ? 4 HKL-2000 'data reduction' . ? 5 HKL-2000 'data scaling' . ? 6 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CG _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 HIS _pdbx_validate_rmsd_bond.auth_seq_id_1 108 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CD2 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 HIS _pdbx_validate_rmsd_bond.auth_seq_id_2 108 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.408 _pdbx_validate_rmsd_bond.bond_target_value 1.354 _pdbx_validate_rmsd_bond.bond_deviation 0.054 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.009 _pdbx_validate_rmsd_bond.linker_flag N # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id VAL _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 16 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -117.52 _pdbx_validate_torsion.psi -115.88 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "3'-deoxy-3'-(L-threonylamino)adenosine" A3T 3 'MAGNESIUM ION' MG 4 water HOH #