data_3VJ7 # _entry.id 3VJ7 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3VJ7 pdb_00003vj7 10.2210/pdb3vj7/pdb RCSB RCSB095111 ? ? WWPDB D_1000095111 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2DJH 'wild type of this protein' unspecified PDB 2DFX 'complex structure of the wild type protein and its inhibitor protein' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3VJ7 _pdbx_database_status.recvd_initial_deposition_date 2011-10-13 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yajima, S.' 1 'Inoue, S.' 2 'Fushinobu, S.' 3 'Ogawa, T.' 4 'Hidaka, M.' 5 'Masaki, H.' 6 # _citation.id primary _citation.title 'Identification of the catalytic residues of sequence-specific and histidine-free ribonuclease colicin E5' _citation.journal_abbrev J.Biochem. _citation.journal_volume 152 _citation.page_first 365 _citation.page_last 372 _citation.year 2012 _citation.journal_id_ASTM ? _citation.country JP _citation.journal_id_ISSN 0021-924X _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22815490 _citation.pdbx_database_id_DOI 10.1093/jb/mvs077 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Inoue-Ito, S.' 1 ? primary 'Yajima, S.' 2 ? primary 'Fushinobu, S.' 3 ? primary 'Nakamura, S.' 4 ? primary 'Ogawa, T.' 5 ? primary 'Hidaka, M.' 6 ? primary 'Masaki, H.' 7 ? # _cell.entry_id 3VJ7 _cell.length_a 29.688 _cell.length_b 49.450 _cell.length_c 64.619 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _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 3VJ7 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 Colicin-E5 12693.945 1 3.1.-.- R33Q 'C-terminal ribonuclease domain, UNP residues 66-180' ? 2 non-polymer syn '2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE' 347.221 1 ? ? ? ? 3 non-polymer syn ;2'-DEOXYURIDINE 3'-MONOPHOSPHATE ; 308.182 1 ? ? ? ? 4 water nat water 18.015 54 ? ? ? ? # _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 ;AEGKLNDELAKNKGKIPGLKIDQKIRGQMPEQGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKY VVVNDRTGEVTQISDKTDPGWVDDSRIQWGNKNDQ ; _entity_poly.pdbx_seq_one_letter_code_can ;AEGKLNDELAKNKGKIPGLKIDQKIRGQMPEQGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKY VVVNDRTGEVTQISDKTDPGWVDDSRIQWGNKNDQ ; _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 ALA n 1 2 GLU n 1 3 GLY n 1 4 LYS n 1 5 LEU n 1 6 ASN n 1 7 ASP n 1 8 GLU n 1 9 LEU n 1 10 ALA n 1 11 LYS n 1 12 ASN n 1 13 LYS n 1 14 GLY n 1 15 LYS n 1 16 ILE n 1 17 PRO n 1 18 GLY n 1 19 LEU n 1 20 LYS n 1 21 ILE n 1 22 ASP n 1 23 GLN n 1 24 LYS n 1 25 ILE n 1 26 ARG n 1 27 GLY n 1 28 GLN n 1 29 MET n 1 30 PRO n 1 31 GLU n 1 32 GLN n 1 33 GLY n 1 34 TRP n 1 35 THR n 1 36 GLU n 1 37 ASP n 1 38 ASP n 1 39 ILE n 1 40 LYS n 1 41 ASN n 1 42 THR n 1 43 VAL n 1 44 SER n 1 45 ASN n 1 46 GLY n 1 47 ALA n 1 48 THR n 1 49 GLY n 1 50 THR n 1 51 SER n 1 52 PHE n 1 53 ASP n 1 54 LYS n 1 55 ARG n 1 56 SER n 1 57 PRO n 1 58 LYS n 1 59 LYS n 1 60 THR n 1 61 PRO n 1 62 PRO n 1 63 ASP n 1 64 TYR n 1 65 LEU n 1 66 GLY n 1 67 ARG n 1 68 ASN n 1 69 ASP n 1 70 PRO n 1 71 ALA n 1 72 THR n 1 73 VAL n 1 74 TYR n 1 75 GLY n 1 76 SER n 1 77 PRO n 1 78 GLY n 1 79 LYS n 1 80 TYR n 1 81 VAL n 1 82 VAL n 1 83 VAL n 1 84 ASN n 1 85 ASP n 1 86 ARG n 1 87 THR n 1 88 GLY n 1 89 GLU n 1 90 VAL n 1 91 THR n 1 92 GLN n 1 93 ILE n 1 94 SER n 1 95 ASP n 1 96 LYS n 1 97 THR n 1 98 ASP n 1 99 PRO n 1 100 GLY n 1 101 TRP n 1 102 VAL n 1 103 ASP n 1 104 ASP n 1 105 SER n 1 106 ARG n 1 107 ILE n 1 108 GLN n 1 109 TRP n 1 110 GLY n 1 111 ASN n 1 112 LYS n 1 113 ASN n 1 114 ASP n 1 115 GLN 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 col _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' _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 CEA5_ECOLX _struct_ref.pdbx_db_accession P18000 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;AEGKLNDELAKNKGKIPGLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKY VVVNDRTGEVTQISDKTDPGWVDDSRIQWGNKNDQ ; _struct_ref.pdbx_align_begin 66 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3VJ7 _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 115 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P18000 _struct_ref_seq.db_align_beg 66 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 180 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 116 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3VJ7 _struct_ref_seq_dif.mon_id GLN _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 32 _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 P18000 _struct_ref_seq_dif.db_mon_id ARG _struct_ref_seq_dif.pdbx_seq_db_seq_num 97 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 33 _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 3PD non-polymer . '2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE' "2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE" 'C10 H14 N5 O7 P' 347.221 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 UM3 non-polymer . ;2'-DEOXYURIDINE 3'-MONOPHOSPHATE ; ? 'C9 H13 N2 O8 P' 308.182 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3VJ7 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.87 _exptl_crystal.density_percent_sol 34.16 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8 _exptl_crystal_grow.pdbx_details '2M ammonium sulfate, 20mM TrisCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 298 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'MAC Science DIP-2030' _diffrn_detector.pdbx_collection_date 1999-11-28 _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 MACSCIENCE _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 3VJ7 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.3 _reflns.number_obs 4574 _reflns.number_all 4583 _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.3 _reflns_shell.d_res_low 2.38 _reflns_shell.percent_possible_all 98.8 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3VJ7 _refine.ls_number_reflns_obs 4307 _refine.ls_number_reflns_all 4340 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 39.27 _refine.ls_d_res_high 2.30 _refine.ls_percent_reflns_obs 99.25 _refine.ls_R_factor_obs 0.23888 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23801 _refine.ls_R_factor_R_free 0.25730 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 207 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.902 _refine.correlation_coeff_Fo_to_Fc_free 0.875 _refine.B_iso_mean 21.526 _refine.aniso_B[1][1] -1.02 _refine.aniso_B[2][2] -0.08 _refine.aniso_B[3][3] 1.10 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _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 ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 2DJH _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_Free 0.264 _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _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 730 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 42 _refine_hist.number_atoms_solvent 54 _refine_hist.number_atoms_total 826 _refine_hist.d_res_high 2.30 _refine_hist.d_res_low 39.27 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.013 0.022 ? 793 ? 'X-RAY DIFFRACTION' r_bond_other_d ? ? ? ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.833 2.002 ? 1065 ? 'X-RAY DIFFRACTION' r_angle_other_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 1.365 5.000 ? 93 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 36.446 25.143 ? 35 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 12.983 15.000 ? 124 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 21.948 15.000 ? 5 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.114 0.200 ? 109 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.010 0.021 ? 602 ? '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 1.509 1.500 ? 467 ? 'X-RAY DIFFRACTION' r_mcbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_it 2.640 2.000 ? 760 ? 'X-RAY DIFFRACTION' r_scbond_it 2.301 3.000 ? 326 ? 'X-RAY DIFFRACTION' r_scangle_it 3.534 4.500 ? 305 ? 'X-RAY DIFFRACTION' r_rigid_bond_restr ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_free ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded ? ? ? ? ? '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 2.301 _refine_ls_shell.d_res_low 2.360 _refine_ls_shell.number_reflns_R_work 301 _refine_ls_shell.R_factor_R_work 0.233 _refine_ls_shell.percent_reflns_obs 99.06 _refine_ls_shell.R_factor_R_free 0.279 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 14 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 3VJ7 _struct.title 'Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 R33Q mutant' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3VJ7 _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'ribonuclease, Hydrolase' # 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 ASP A 22 ? GLY A 33 ? ASP A 23 GLY A 34 1 ? 12 HELX_P HELX_P2 2 THR A 35 ? ASN A 45 ? THR A 36 ASN A 46 1 ? 11 HELX_P HELX_P3 3 SER A 56 ? THR A 60 ? SER A 57 THR A 61 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_conn.id covale1 _struct_conn.conn_type_id covale _struct_conn.pdbx_leaving_atom_flag none _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_comp_id 3PD _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_label_atom_id P _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 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_comp_id UM3 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_label_atom_id "O5'" _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id 3PD _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id UM3 _struct_conn.ptnr2_auth_seq_id 117 _struct_conn.ptnr2_symmetry 1_555 _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 1.590 _struct_conn.pdbx_value_order ? _struct_conn.pdbx_role ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 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 VAL A 90 ? ILE A 93 ? VAL A 91 ILE A 94 A 2 LYS A 79 ? ASN A 84 ? LYS A 80 ASN A 85 A 3 ASP A 69 ? SER A 76 ? ASP A 70 SER A 77 A 4 ALA A 47 ? ASP A 53 ? ALA A 48 ASP A 54 A 5 GLN A 108 ? TRP A 109 ? GLN A 109 TRP A 110 # 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 THR A 91 ? O THR A 92 N VAL A 82 ? N VAL A 83 A 2 3 O LYS A 79 ? O LYS A 80 N SER A 76 ? N SER A 77 A 3 4 O ASP A 69 ? O ASP A 70 N ASP A 53 ? N ASP A 54 A 4 5 N THR A 50 ? N THR A 51 O GLN A 108 ? O GLN A 109 # 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 A 3PD 1 ? 13 'BINDING SITE FOR RESIDUE 3PD A 1' AC2 Software A UM3 117 ? 16 'BINDING SITE FOR RESIDUE UM3 A 117' # 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 13 LYS A 24 ? LYS A 25 . ? 1_555 ? 2 AC1 13 GLN A 28 ? GLN A 29 . ? 1_555 ? 3 AC1 13 PHE A 52 ? PHE A 53 . ? 4_555 ? 4 AC1 13 LYS A 54 ? LYS A 55 . ? 4_555 ? 5 AC1 13 GLN A 92 ? GLN A 93 . ? 1_555 ? 6 AC1 13 TRP A 101 ? TRP A 102 . ? 1_555 ? 7 AC1 13 VAL A 102 ? VAL A 103 . ? 1_555 ? 8 AC1 13 SER A 105 ? SER A 106 . ? 4_555 ? 9 AC1 13 ARG A 106 ? ARG A 107 . ? 4_555 ? 10 AC1 13 GLN A 108 ? GLN A 109 . ? 4_555 ? 11 AC1 13 UM3 C . ? UM3 A 117 . ? 1_555 ? 12 AC1 13 HOH D . ? HOH A 125 . ? 1_555 ? 13 AC1 13 HOH D . ? HOH A 146 . ? 1_555 ? 14 AC2 16 3PD B . ? 3PD A 1 . ? 1_555 ? 15 AC2 16 LYS A 24 ? LYS A 25 . ? 1_555 ? 16 AC2 16 SER A 51 ? SER A 52 . ? 1_555 ? 17 AC2 16 PHE A 52 ? PHE A 53 . ? 1_555 ? 18 AC2 16 ASP A 53 ? ASP A 54 . ? 1_555 ? 19 AC2 16 LYS A 54 ? LYS A 55 . ? 1_555 ? 20 AC2 16 ARG A 55 ? ARG A 56 . ? 1_555 ? 21 AC2 16 SER A 56 ? SER A 57 . ? 1_555 ? 22 AC2 16 LYS A 59 ? LYS A 60 . ? 1_555 ? 23 AC2 16 VAL A 82 ? VAL A 83 . ? 1_555 ? 24 AC2 16 THR A 91 ? THR A 92 . ? 1_555 ? 25 AC2 16 GLN A 92 ? GLN A 93 . ? 1_555 ? 26 AC2 16 ASP A 104 ? ASP A 105 . ? 1_555 ? 27 AC2 16 ARG A 106 ? ARG A 107 . ? 1_555 ? 28 AC2 16 GLN A 108 ? GLN A 109 . ? 4_555 ? 29 AC2 16 HOH D . ? HOH A 138 . ? 1_555 ? # _database_PDB_matrix.entry_id 3VJ7 _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 3VJ7 _atom_sites.fract_transf_matrix[1][1] 0.033684 _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] 0.020222 _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] 0.015475 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ALA 1 2 ? ? ? A . n A 1 2 GLU 2 3 ? ? ? A . n A 1 3 GLY 3 4 ? ? ? A . n A 1 4 LYS 4 5 ? ? ? A . n A 1 5 LEU 5 6 ? ? ? A . n A 1 6 ASN 6 7 ? ? ? A . n A 1 7 ASP 7 8 ? ? ? A . n A 1 8 GLU 8 9 ? ? ? A . n A 1 9 LEU 9 10 ? ? ? A . n A 1 10 ALA 10 11 ? ? ? A . n A 1 11 LYS 11 12 ? ? ? A . n A 1 12 ASN 12 13 ? ? ? A . n A 1 13 LYS 13 14 ? ? ? A . n A 1 14 GLY 14 15 ? ? ? A . n A 1 15 LYS 15 16 ? ? ? A . n A 1 16 ILE 16 17 ? ? ? A . n A 1 17 PRO 17 18 18 PRO PRO A . n A 1 18 GLY 18 19 19 GLY GLY A . n A 1 19 LEU 19 20 20 LEU LEU A . n A 1 20 LYS 20 21 21 LYS LYS A . n A 1 21 ILE 21 22 22 ILE ILE A . n A 1 22 ASP 22 23 23 ASP ASP A . n A 1 23 GLN 23 24 24 GLN GLN A . n A 1 24 LYS 24 25 25 LYS LYS A . n A 1 25 ILE 25 26 26 ILE ILE A . n A 1 26 ARG 26 27 27 ARG ARG A . n A 1 27 GLY 27 28 28 GLY GLY A . n A 1 28 GLN 28 29 29 GLN GLN A . n A 1 29 MET 29 30 30 MET MET A . n A 1 30 PRO 30 31 31 PRO PRO A . n A 1 31 GLU 31 32 32 GLU GLU A . n A 1 32 GLN 32 33 33 GLN GLN A . n A 1 33 GLY 33 34 34 GLY GLY A . n A 1 34 TRP 34 35 35 TRP TRP A . n A 1 35 THR 35 36 36 THR THR A . n A 1 36 GLU 36 37 37 GLU GLU A . n A 1 37 ASP 37 38 38 ASP ASP A . n A 1 38 ASP 38 39 39 ASP ASP A . n A 1 39 ILE 39 40 40 ILE ILE A . n A 1 40 LYS 40 41 41 LYS LYS A . n A 1 41 ASN 41 42 42 ASN ASN A . n A 1 42 THR 42 43 43 THR THR A . n A 1 43 VAL 43 44 44 VAL VAL A . n A 1 44 SER 44 45 45 SER SER A . n A 1 45 ASN 45 46 46 ASN ASN A . n A 1 46 GLY 46 47 47 GLY GLY A . n A 1 47 ALA 47 48 48 ALA ALA A . n A 1 48 THR 48 49 49 THR THR A . n A 1 49 GLY 49 50 50 GLY GLY A . n A 1 50 THR 50 51 51 THR THR A . n A 1 51 SER 51 52 52 SER SER A . n A 1 52 PHE 52 53 53 PHE PHE A . n A 1 53 ASP 53 54 54 ASP ASP A . n A 1 54 LYS 54 55 55 LYS LYS A . n A 1 55 ARG 55 56 56 ARG ARG A . n A 1 56 SER 56 57 57 SER SER A . n A 1 57 PRO 57 58 58 PRO PRO A . n A 1 58 LYS 58 59 59 LYS LYS A . n A 1 59 LYS 59 60 60 LYS LYS A . n A 1 60 THR 60 61 61 THR THR A . n A 1 61 PRO 61 62 62 PRO PRO A . n A 1 62 PRO 62 63 63 PRO PRO A . n A 1 63 ASP 63 64 64 ASP ASP A . n A 1 64 TYR 64 65 65 TYR TYR A . n A 1 65 LEU 65 66 66 LEU LEU A . n A 1 66 GLY 66 67 67 GLY GLY A . n A 1 67 ARG 67 68 68 ARG ARG A . n A 1 68 ASN 68 69 69 ASN ASN A . n A 1 69 ASP 69 70 70 ASP ASP A . n A 1 70 PRO 70 71 71 PRO PRO A . n A 1 71 ALA 71 72 72 ALA ALA A . n A 1 72 THR 72 73 73 THR THR A . n A 1 73 VAL 73 74 74 VAL VAL A . n A 1 74 TYR 74 75 75 TYR TYR A . n A 1 75 GLY 75 76 76 GLY GLY A . n A 1 76 SER 76 77 77 SER SER A . n A 1 77 PRO 77 78 78 PRO PRO A . n A 1 78 GLY 78 79 79 GLY GLY A . n A 1 79 LYS 79 80 80 LYS LYS A . n A 1 80 TYR 80 81 81 TYR TYR A . n A 1 81 VAL 81 82 82 VAL VAL A . n A 1 82 VAL 82 83 83 VAL VAL A . n A 1 83 VAL 83 84 84 VAL VAL A . n A 1 84 ASN 84 85 85 ASN ASN A . n A 1 85 ASP 85 86 86 ASP ASP A . n A 1 86 ARG 86 87 87 ARG ARG A . n A 1 87 THR 87 88 88 THR THR A . n A 1 88 GLY 88 89 89 GLY GLY A . n A 1 89 GLU 89 90 90 GLU GLU A . n A 1 90 VAL 90 91 91 VAL VAL A . n A 1 91 THR 91 92 92 THR THR A . n A 1 92 GLN 92 93 93 GLN GLN A . n A 1 93 ILE 93 94 94 ILE ILE A . n A 1 94 SER 94 95 95 SER SER A . n A 1 95 ASP 95 96 96 ASP ASP A . n A 1 96 LYS 96 97 97 LYS LYS A . n A 1 97 THR 97 98 98 THR THR A . n A 1 98 ASP 98 99 99 ASP ASP A . n A 1 99 PRO 99 100 100 PRO PRO A . n A 1 100 GLY 100 101 101 GLY GLY A . n A 1 101 TRP 101 102 102 TRP TRP A . n A 1 102 VAL 102 103 103 VAL VAL A . n A 1 103 ASP 103 104 104 ASP ASP A . n A 1 104 ASP 104 105 105 ASP ASP A . n A 1 105 SER 105 106 106 SER SER A . n A 1 106 ARG 106 107 107 ARG ARG A . n A 1 107 ILE 107 108 108 ILE ILE A . n A 1 108 GLN 108 109 109 GLN GLN A . n A 1 109 TRP 109 110 110 TRP TRP A . n A 1 110 GLY 110 111 111 GLY GLY A . n A 1 111 ASN 111 112 ? ? ? A . n A 1 112 LYS 112 113 ? ? ? A . n A 1 113 ASN 113 114 ? ? ? A . n A 1 114 ASP 114 115 ? ? ? A . n A 1 115 GLN 115 116 ? ? ? 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 3PD 1 1 1 3PD 3PD A . C 3 UM3 1 117 1 UM3 UM3 A . D 4 HOH 1 118 1 HOH HOH A . D 4 HOH 2 119 2 HOH HOH A . D 4 HOH 3 120 3 HOH HOH A . D 4 HOH 4 121 4 HOH HOH A . D 4 HOH 5 122 5 HOH HOH A . D 4 HOH 6 123 6 HOH HOH A . D 4 HOH 7 124 7 HOH HOH A . D 4 HOH 8 125 8 HOH HOH A . D 4 HOH 9 126 9 HOH HOH A . D 4 HOH 10 127 10 HOH HOH A . D 4 HOH 11 128 11 HOH HOH A . D 4 HOH 12 129 12 HOH HOH A . D 4 HOH 13 130 13 HOH HOH A . D 4 HOH 14 131 14 HOH HOH A . D 4 HOH 15 132 15 HOH HOH A . D 4 HOH 16 133 16 HOH HOH A . D 4 HOH 17 134 17 HOH HOH A . D 4 HOH 18 135 18 HOH HOH A . D 4 HOH 19 136 19 HOH HOH A . D 4 HOH 20 137 20 HOH HOH A . D 4 HOH 21 138 21 HOH HOH A . D 4 HOH 22 139 22 HOH HOH A . D 4 HOH 23 140 23 HOH HOH A . D 4 HOH 24 141 24 HOH HOH A . D 4 HOH 25 142 25 HOH HOH A . D 4 HOH 26 143 26 HOH HOH A . D 4 HOH 27 144 27 HOH HOH A . D 4 HOH 28 145 28 HOH HOH A . D 4 HOH 29 146 29 HOH HOH A . D 4 HOH 30 147 30 HOH HOH A . D 4 HOH 31 148 31 HOH HOH A . D 4 HOH 32 149 32 HOH HOH A . D 4 HOH 33 150 33 HOH HOH A . D 4 HOH 34 151 34 HOH HOH A . D 4 HOH 35 152 35 HOH HOH A . D 4 HOH 36 153 36 HOH HOH A . D 4 HOH 37 154 37 HOH HOH A . D 4 HOH 38 155 38 HOH HOH A . D 4 HOH 39 156 39 HOH HOH A . D 4 HOH 40 157 40 HOH HOH A . D 4 HOH 41 158 41 HOH HOH A . D 4 HOH 42 159 42 HOH HOH A . D 4 HOH 43 160 43 HOH HOH A . D 4 HOH 44 161 44 HOH HOH A . D 4 HOH 45 162 45 HOH HOH A . D 4 HOH 46 163 46 HOH HOH A . D 4 HOH 47 164 47 HOH HOH A . D 4 HOH 48 165 48 HOH HOH A . D 4 HOH 49 166 49 HOH HOH A . D 4 HOH 50 167 50 HOH HOH A . D 4 HOH 51 168 51 HOH HOH A . D 4 HOH 52 169 52 HOH HOH A . D 4 HOH 53 170 53 HOH HOH A . D 4 HOH 54 171 54 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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-11-02 2 'Structure model' 1 1 2013-02-06 3 'Structure model' 1 2 2023-11-08 # _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_details.details ? # 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_ref_seq_dif 7 3 'Structure model' struct_site # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ref_seq_dif.details' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DIP-2030 'data collection' . ? 1 AMoRE phasing . ? 2 CNS refinement 1.0 ? 3 DENZO 'data reduction' . ? 4 SCALEPACK 'data scaling' . ? 5 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 C _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 THR _pdbx_validate_rmsd_angle.auth_seq_id_1 61 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 N _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 PRO _pdbx_validate_rmsd_angle.auth_seq_id_2 62 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 CA _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 PRO _pdbx_validate_rmsd_angle.auth_seq_id_3 62 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 129.86 _pdbx_validate_rmsd_angle.angle_target_value 119.30 _pdbx_validate_rmsd_angle.angle_deviation 10.56 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.50 _pdbx_validate_rmsd_angle.linker_flag 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 SER A 52 ? ? -174.98 -156.92 2 1 PRO A 62 ? ? -22.94 169.40 3 1 PRO A 63 ? ? 13.52 58.68 4 1 ASP A 64 ? ? -179.44 -62.51 5 1 ASN A 69 ? ? -147.15 56.63 # 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 2 ? A ALA 1 2 1 Y 1 A GLU 3 ? A GLU 2 3 1 Y 1 A GLY 4 ? A GLY 3 4 1 Y 1 A LYS 5 ? A LYS 4 5 1 Y 1 A LEU 6 ? A LEU 5 6 1 Y 1 A ASN 7 ? A ASN 6 7 1 Y 1 A ASP 8 ? A ASP 7 8 1 Y 1 A GLU 9 ? A GLU 8 9 1 Y 1 A LEU 10 ? A LEU 9 10 1 Y 1 A ALA 11 ? A ALA 10 11 1 Y 1 A LYS 12 ? A LYS 11 12 1 Y 1 A ASN 13 ? A ASN 12 13 1 Y 1 A LYS 14 ? A LYS 13 14 1 Y 1 A GLY 15 ? A GLY 14 15 1 Y 1 A LYS 16 ? A LYS 15 16 1 Y 1 A ILE 17 ? A ILE 16 17 1 Y 1 A ASN 112 ? A ASN 111 18 1 Y 1 A LYS 113 ? A LYS 112 19 1 Y 1 A ASN 114 ? A ASN 113 20 1 Y 1 A ASP 115 ? A ASP 114 21 1 Y 1 A GLN 116 ? A GLN 115 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 3PD "O5'" O N N 1 3PD "C5'" C N N 2 3PD "C4'" C N R 3 3PD "O4'" O N N 4 3PD "C1'" C N R 5 3PD "C2'" C N N 6 3PD "C3'" C N S 7 3PD "O3'" O N N 8 3PD N9 N Y N 9 3PD C4 C Y N 10 3PD N3 N Y N 11 3PD C2 C Y N 12 3PD N2 N N N 13 3PD N1 N Y N 14 3PD C6 C Y N 15 3PD O6 O N N 16 3PD C5 C Y N 17 3PD N7 N Y N 18 3PD C8 C Y N 19 3PD P P N N 20 3PD O1P O N N 21 3PD O2P O N N 22 3PD O1 O N N 23 3PD "H5'" H N N 24 3PD "H5'1" H N N 25 3PD "H5'2" H N N 26 3PD "H4'" H N N 27 3PD "H1'" H N N 28 3PD "H2'1" H N N 29 3PD "H2'2" H N N 30 3PD "H3'" H N N 31 3PD HN21 H N N 32 3PD HN22 H N N 33 3PD HN1 H N N 34 3PD H8 H N N 35 3PD H1P H N N 36 3PD H2P H N N 37 ALA N N N N 38 ALA CA C N S 39 ALA C C N N 40 ALA O O N N 41 ALA CB C N N 42 ALA OXT O N N 43 ALA H H N N 44 ALA H2 H N N 45 ALA HA H N N 46 ALA HB1 H N N 47 ALA HB2 H N N 48 ALA HB3 H N N 49 ALA HXT H N N 50 ARG N N N N 51 ARG CA C N S 52 ARG C C N N 53 ARG O O N N 54 ARG CB C N N 55 ARG CG C N N 56 ARG CD C N N 57 ARG NE N N N 58 ARG CZ C N N 59 ARG NH1 N N N 60 ARG NH2 N N N 61 ARG OXT O N N 62 ARG H H N N 63 ARG H2 H N N 64 ARG HA H N N 65 ARG HB2 H N N 66 ARG HB3 H N N 67 ARG HG2 H N N 68 ARG HG3 H N N 69 ARG HD2 H N N 70 ARG HD3 H N N 71 ARG HE H N N 72 ARG HH11 H N N 73 ARG HH12 H N N 74 ARG HH21 H N N 75 ARG HH22 H N N 76 ARG HXT H N N 77 ASN N N N N 78 ASN CA C N S 79 ASN C C N N 80 ASN O O N N 81 ASN CB C N N 82 ASN CG C N N 83 ASN OD1 O N N 84 ASN ND2 N N N 85 ASN OXT O N N 86 ASN H H N N 87 ASN H2 H N N 88 ASN HA H N N 89 ASN HB2 H N N 90 ASN HB3 H N N 91 ASN HD21 H N N 92 ASN HD22 H N N 93 ASN HXT H N N 94 ASP N N N N 95 ASP CA C N S 96 ASP C C N N 97 ASP O O N N 98 ASP CB C N N 99 ASP CG C N N 100 ASP OD1 O N N 101 ASP OD2 O N N 102 ASP OXT O N N 103 ASP H H N N 104 ASP H2 H N N 105 ASP HA H N N 106 ASP HB2 H N N 107 ASP HB3 H N N 108 ASP HD2 H N N 109 ASP HXT H N N 110 GLN N N N N 111 GLN CA C N S 112 GLN C C N N 113 GLN O O N N 114 GLN CB C N N 115 GLN CG C N N 116 GLN CD C N N 117 GLN OE1 O N N 118 GLN NE2 N N N 119 GLN OXT O N N 120 GLN H H N N 121 GLN H2 H N N 122 GLN HA H N N 123 GLN HB2 H N N 124 GLN HB3 H N N 125 GLN HG2 H N N 126 GLN HG3 H N N 127 GLN HE21 H N N 128 GLN HE22 H N N 129 GLN HXT H N N 130 GLU N N N N 131 GLU CA C N S 132 GLU C C N N 133 GLU O O N N 134 GLU CB C N N 135 GLU CG C N N 136 GLU CD C N N 137 GLU OE1 O N N 138 GLU OE2 O N N 139 GLU OXT O N N 140 GLU H H N N 141 GLU H2 H N N 142 GLU HA H N N 143 GLU HB2 H N N 144 GLU HB3 H N N 145 GLU HG2 H N N 146 GLU HG3 H N N 147 GLU HE2 H N N 148 GLU HXT H N N 149 GLY N N N N 150 GLY CA C N N 151 GLY C C N N 152 GLY O O N N 153 GLY OXT O N N 154 GLY H H N N 155 GLY H2 H N N 156 GLY HA2 H N N 157 GLY HA3 H N N 158 GLY HXT H N N 159 HOH O O N N 160 HOH H1 H N N 161 HOH H2 H N N 162 ILE N N N N 163 ILE CA C N S 164 ILE C C N N 165 ILE O O N N 166 ILE CB C N S 167 ILE CG1 C N N 168 ILE CG2 C N N 169 ILE CD1 C N N 170 ILE OXT O N N 171 ILE H H N N 172 ILE H2 H N N 173 ILE HA H N N 174 ILE HB H N N 175 ILE HG12 H N N 176 ILE HG13 H N N 177 ILE HG21 H N N 178 ILE HG22 H N N 179 ILE HG23 H N N 180 ILE HD11 H N N 181 ILE HD12 H N N 182 ILE HD13 H N N 183 ILE HXT H N N 184 LEU N N N N 185 LEU CA C N S 186 LEU C C N N 187 LEU O O N N 188 LEU CB C N N 189 LEU CG C N N 190 LEU CD1 C N N 191 LEU CD2 C N N 192 LEU OXT O N N 193 LEU H H N N 194 LEU H2 H N N 195 LEU HA H N N 196 LEU HB2 H N N 197 LEU HB3 H N N 198 LEU HG H N N 199 LEU HD11 H N N 200 LEU HD12 H N N 201 LEU HD13 H N N 202 LEU HD21 H N N 203 LEU HD22 H N N 204 LEU HD23 H N N 205 LEU HXT H N N 206 LYS N N N N 207 LYS CA C N S 208 LYS C C N N 209 LYS O O N N 210 LYS CB C N N 211 LYS CG C N N 212 LYS CD C N N 213 LYS CE C N N 214 LYS NZ N N N 215 LYS OXT O N N 216 LYS H H N N 217 LYS H2 H N N 218 LYS HA H N N 219 LYS HB2 H N N 220 LYS HB3 H N N 221 LYS HG2 H N N 222 LYS HG3 H N N 223 LYS HD2 H N N 224 LYS HD3 H N N 225 LYS HE2 H N N 226 LYS HE3 H N N 227 LYS HZ1 H N N 228 LYS HZ2 H N N 229 LYS HZ3 H N N 230 LYS HXT H N N 231 MET N N N N 232 MET CA C N S 233 MET C C N N 234 MET O O N N 235 MET CB C N N 236 MET CG C N N 237 MET SD S N N 238 MET CE C N N 239 MET OXT O N N 240 MET H H N N 241 MET H2 H N N 242 MET HA H N N 243 MET HB2 H N N 244 MET HB3 H N N 245 MET HG2 H N N 246 MET HG3 H N N 247 MET HE1 H N N 248 MET HE2 H N N 249 MET HE3 H N N 250 MET HXT H N N 251 PHE N N N N 252 PHE CA C N S 253 PHE C C N N 254 PHE O O N N 255 PHE CB C N N 256 PHE CG C Y N 257 PHE CD1 C Y N 258 PHE CD2 C Y N 259 PHE CE1 C Y N 260 PHE CE2 C Y N 261 PHE CZ C Y N 262 PHE OXT O N N 263 PHE H H N N 264 PHE H2 H N N 265 PHE HA H N N 266 PHE HB2 H N N 267 PHE HB3 H N N 268 PHE HD1 H N N 269 PHE HD2 H N N 270 PHE HE1 H N N 271 PHE HE2 H N N 272 PHE HZ H N N 273 PHE HXT H N N 274 PRO N N N N 275 PRO CA C N S 276 PRO C C N N 277 PRO O O N N 278 PRO CB C N N 279 PRO CG C N N 280 PRO CD C N N 281 PRO OXT O N N 282 PRO H H N N 283 PRO HA H N N 284 PRO HB2 H N N 285 PRO HB3 H N N 286 PRO HG2 H N N 287 PRO HG3 H N N 288 PRO HD2 H N N 289 PRO HD3 H N N 290 PRO HXT H N N 291 SER N N N N 292 SER CA C N S 293 SER C C N N 294 SER O O N N 295 SER CB C N N 296 SER OG O N N 297 SER OXT O N N 298 SER H H N N 299 SER H2 H N N 300 SER HA H N N 301 SER HB2 H N N 302 SER HB3 H N N 303 SER HG H N N 304 SER HXT H N N 305 THR N N N N 306 THR CA C N S 307 THR C C N N 308 THR O O N N 309 THR CB C N R 310 THR OG1 O N N 311 THR CG2 C N N 312 THR OXT O N N 313 THR H H N N 314 THR H2 H N N 315 THR HA H N N 316 THR HB H N N 317 THR HG1 H N N 318 THR HG21 H N N 319 THR HG22 H N N 320 THR HG23 H N N 321 THR HXT H N N 322 TRP N N N N 323 TRP CA C N S 324 TRP C C N N 325 TRP O O N N 326 TRP CB C N N 327 TRP CG C Y N 328 TRP CD1 C Y N 329 TRP CD2 C Y N 330 TRP NE1 N Y N 331 TRP CE2 C Y N 332 TRP CE3 C Y N 333 TRP CZ2 C Y N 334 TRP CZ3 C Y N 335 TRP CH2 C Y N 336 TRP OXT O N N 337 TRP H H N N 338 TRP H2 H N N 339 TRP HA H N N 340 TRP HB2 H N N 341 TRP HB3 H N N 342 TRP HD1 H N N 343 TRP HE1 H N N 344 TRP HE3 H N N 345 TRP HZ2 H N N 346 TRP HZ3 H N N 347 TRP HH2 H N N 348 TRP HXT H N N 349 TYR N N N N 350 TYR CA C N S 351 TYR C C N N 352 TYR O O N N 353 TYR CB C N N 354 TYR CG C Y N 355 TYR CD1 C Y N 356 TYR CD2 C Y N 357 TYR CE1 C Y N 358 TYR CE2 C Y N 359 TYR CZ C Y N 360 TYR OH O N N 361 TYR OXT O N N 362 TYR H H N N 363 TYR H2 H N N 364 TYR HA H N N 365 TYR HB2 H N N 366 TYR HB3 H N N 367 TYR HD1 H N N 368 TYR HD2 H N N 369 TYR HE1 H N N 370 TYR HE2 H N N 371 TYR HH H N N 372 TYR HXT H N N 373 UM3 N1 N Y N 374 UM3 C2 C Y N 375 UM3 N3 N Y N 376 UM3 C4 C Y N 377 UM3 C5 C Y N 378 UM3 C6 C Y N 379 UM3 O2 O N N 380 UM3 O4 O N N 381 UM3 "C1'" C N R 382 UM3 "C2'" C N N 383 UM3 "C3'" C N S 384 UM3 "C4'" C N R 385 UM3 "O3'" O N N 386 UM3 "O4'" O N N 387 UM3 "C5'" C N N 388 UM3 "O5'" O N N 389 UM3 P P N N 390 UM3 O1P O N N 391 UM3 O2P O N N 392 UM3 O3P O N N 393 UM3 HN3 H N N 394 UM3 H5 H N N 395 UM3 H6 H N N 396 UM3 "H1'" H N N 397 UM3 "H2'1" H N N 398 UM3 "H2'2" H N N 399 UM3 "H3'" H N N 400 UM3 "H4'" H N N 401 UM3 "H5'1" H N N 402 UM3 "H5'2" H N N 403 UM3 "HO5'" H N N 404 UM3 HOP2 H N N 405 UM3 HOP3 H N N 406 VAL N N N N 407 VAL CA C N S 408 VAL C C N N 409 VAL O O N N 410 VAL CB C N N 411 VAL CG1 C N N 412 VAL CG2 C N N 413 VAL OXT O N N 414 VAL H H N N 415 VAL H2 H N N 416 VAL HA H N N 417 VAL HB H N N 418 VAL HG11 H N N 419 VAL HG12 H N N 420 VAL HG13 H N N 421 VAL HG21 H N N 422 VAL HG22 H N N 423 VAL HG23 H N N 424 VAL HXT H N N 425 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 3PD "O5'" "C5'" sing N N 1 3PD "O5'" "H5'" sing N N 2 3PD "C5'" "C4'" sing N N 3 3PD "C5'" "H5'1" sing N N 4 3PD "C5'" "H5'2" sing N N 5 3PD "C4'" "O4'" sing N N 6 3PD "C4'" "C3'" sing N N 7 3PD "C4'" "H4'" sing N N 8 3PD "O4'" "C1'" sing N N 9 3PD "C1'" "C2'" sing N N 10 3PD "C1'" N9 sing N N 11 3PD "C1'" "H1'" sing N N 12 3PD "C2'" "C3'" sing N N 13 3PD "C2'" "H2'1" sing N N 14 3PD "C2'" "H2'2" sing N N 15 3PD "C3'" "O3'" sing N N 16 3PD "C3'" "H3'" sing N N 17 3PD "O3'" P sing N N 18 3PD N9 C4 sing Y N 19 3PD N9 C8 sing Y N 20 3PD C4 N3 sing Y N 21 3PD C4 C5 doub Y N 22 3PD N3 C2 doub Y N 23 3PD C2 N2 sing N N 24 3PD C2 N1 sing Y N 25 3PD N2 HN21 sing N N 26 3PD N2 HN22 sing N N 27 3PD N1 C6 sing Y N 28 3PD N1 HN1 sing N N 29 3PD C6 O6 doub N N 30 3PD C6 C5 sing Y N 31 3PD C5 N7 sing Y N 32 3PD N7 C8 doub Y N 33 3PD C8 H8 sing N N 34 3PD P O1P sing N N 35 3PD P O2P sing N N 36 3PD P O1 doub N N 37 3PD O1P H1P sing N N 38 3PD O2P H2P sing N N 39 ALA N CA sing N N 40 ALA N H sing N N 41 ALA N H2 sing N N 42 ALA CA C sing N N 43 ALA CA CB sing N N 44 ALA CA HA sing N N 45 ALA C O doub N N 46 ALA C OXT sing N N 47 ALA CB HB1 sing N N 48 ALA CB HB2 sing N N 49 ALA CB HB3 sing N N 50 ALA OXT HXT sing N N 51 ARG N CA sing N N 52 ARG N H sing N N 53 ARG N H2 sing N N 54 ARG CA C sing N N 55 ARG CA CB sing N N 56 ARG CA HA sing N N 57 ARG C O doub N N 58 ARG C OXT sing N N 59 ARG CB CG sing N N 60 ARG CB HB2 sing N N 61 ARG CB HB3 sing N N 62 ARG CG CD sing N N 63 ARG CG HG2 sing N N 64 ARG CG HG3 sing N N 65 ARG CD NE sing N N 66 ARG CD HD2 sing N N 67 ARG CD HD3 sing N N 68 ARG NE CZ sing N N 69 ARG NE HE sing N N 70 ARG CZ NH1 sing N N 71 ARG CZ NH2 doub N N 72 ARG NH1 HH11 sing N N 73 ARG NH1 HH12 sing N N 74 ARG NH2 HH21 sing N N 75 ARG NH2 HH22 sing N N 76 ARG OXT HXT sing N N 77 ASN N CA sing N N 78 ASN N H sing N N 79 ASN N H2 sing N N 80 ASN CA C sing N N 81 ASN CA CB sing N N 82 ASN CA HA sing N N 83 ASN C O doub N N 84 ASN C OXT sing N N 85 ASN CB CG sing N N 86 ASN CB HB2 sing N N 87 ASN CB HB3 sing N N 88 ASN CG OD1 doub N N 89 ASN CG ND2 sing N N 90 ASN ND2 HD21 sing N N 91 ASN ND2 HD22 sing N N 92 ASN OXT HXT sing N N 93 ASP N CA sing N N 94 ASP N H sing N N 95 ASP N H2 sing N N 96 ASP CA C sing N N 97 ASP CA CB sing N N 98 ASP CA HA sing N N 99 ASP C O doub N N 100 ASP C OXT sing N N 101 ASP CB CG sing N N 102 ASP CB HB2 sing N N 103 ASP CB HB3 sing N N 104 ASP CG OD1 doub N N 105 ASP CG OD2 sing N N 106 ASP OD2 HD2 sing N N 107 ASP OXT HXT sing N N 108 GLN N CA sing N N 109 GLN N H sing N N 110 GLN N H2 sing N N 111 GLN CA C sing N N 112 GLN CA CB sing N N 113 GLN CA HA sing N N 114 GLN C O doub N N 115 GLN C OXT sing N N 116 GLN CB CG sing N N 117 GLN CB HB2 sing N N 118 GLN CB HB3 sing N N 119 GLN CG CD sing N N 120 GLN CG HG2 sing N N 121 GLN CG HG3 sing N N 122 GLN CD OE1 doub N N 123 GLN CD NE2 sing N N 124 GLN NE2 HE21 sing N N 125 GLN NE2 HE22 sing N N 126 GLN OXT HXT sing N N 127 GLU N CA sing N N 128 GLU N H sing N N 129 GLU N H2 sing N N 130 GLU CA C sing N N 131 GLU CA CB sing N N 132 GLU CA HA sing N N 133 GLU C O doub N N 134 GLU C OXT sing N N 135 GLU CB CG sing N N 136 GLU CB HB2 sing N N 137 GLU CB HB3 sing N N 138 GLU CG CD sing N N 139 GLU CG HG2 sing N N 140 GLU CG HG3 sing N N 141 GLU CD OE1 doub N N 142 GLU CD OE2 sing N N 143 GLU OE2 HE2 sing N N 144 GLU OXT HXT sing N N 145 GLY N CA sing N N 146 GLY N H sing N N 147 GLY N H2 sing N N 148 GLY CA C sing N N 149 GLY CA HA2 sing N N 150 GLY CA HA3 sing N N 151 GLY C O doub N N 152 GLY C OXT sing N N 153 GLY OXT HXT sing N N 154 HOH O H1 sing N N 155 HOH O H2 sing N N 156 ILE N CA sing N N 157 ILE N H sing N N 158 ILE N H2 sing N N 159 ILE CA C sing N N 160 ILE CA CB sing N N 161 ILE CA HA sing N N 162 ILE C O doub N N 163 ILE C OXT sing N N 164 ILE CB CG1 sing N N 165 ILE CB CG2 sing N N 166 ILE CB HB sing N N 167 ILE CG1 CD1 sing N N 168 ILE CG1 HG12 sing N N 169 ILE CG1 HG13 sing N N 170 ILE CG2 HG21 sing N N 171 ILE CG2 HG22 sing N N 172 ILE CG2 HG23 sing N N 173 ILE CD1 HD11 sing N N 174 ILE CD1 HD12 sing N N 175 ILE CD1 HD13 sing N N 176 ILE OXT HXT sing N N 177 LEU N CA sing N N 178 LEU N H sing N N 179 LEU N H2 sing N N 180 LEU CA C sing N N 181 LEU CA CB sing N N 182 LEU CA HA sing N N 183 LEU C O doub N N 184 LEU C OXT sing N N 185 LEU CB CG sing N N 186 LEU CB HB2 sing N N 187 LEU CB HB3 sing N N 188 LEU CG CD1 sing N N 189 LEU CG CD2 sing N N 190 LEU CG HG sing N N 191 LEU CD1 HD11 sing N N 192 LEU CD1 HD12 sing N N 193 LEU CD1 HD13 sing N N 194 LEU CD2 HD21 sing N N 195 LEU CD2 HD22 sing N N 196 LEU CD2 HD23 sing N N 197 LEU OXT HXT sing N N 198 LYS N CA sing N N 199 LYS N H sing N N 200 LYS N H2 sing N N 201 LYS CA C sing N N 202 LYS CA CB sing N N 203 LYS CA HA sing N N 204 LYS C O doub N N 205 LYS C OXT sing N N 206 LYS CB CG sing N N 207 LYS CB HB2 sing N N 208 LYS CB HB3 sing N N 209 LYS CG CD sing N N 210 LYS CG HG2 sing N N 211 LYS CG HG3 sing N N 212 LYS CD CE sing N N 213 LYS CD HD2 sing N N 214 LYS CD HD3 sing N N 215 LYS CE NZ sing N N 216 LYS CE HE2 sing N N 217 LYS CE HE3 sing N N 218 LYS NZ HZ1 sing N N 219 LYS NZ HZ2 sing N N 220 LYS NZ HZ3 sing N N 221 LYS OXT HXT sing N N 222 MET N CA sing N N 223 MET N H sing N N 224 MET N H2 sing N N 225 MET CA C sing N N 226 MET CA CB sing N N 227 MET CA HA sing N N 228 MET C O doub N N 229 MET C OXT sing N N 230 MET CB CG sing N N 231 MET CB HB2 sing N N 232 MET CB HB3 sing N N 233 MET CG SD sing N N 234 MET CG HG2 sing N N 235 MET CG HG3 sing N N 236 MET SD CE sing N N 237 MET CE HE1 sing N N 238 MET CE HE2 sing N N 239 MET CE HE3 sing N N 240 MET OXT HXT sing N N 241 PHE N CA sing N N 242 PHE N H sing N N 243 PHE N H2 sing N N 244 PHE CA C sing N N 245 PHE CA CB sing N N 246 PHE CA HA sing N N 247 PHE C O doub N N 248 PHE C OXT sing N N 249 PHE CB CG sing N N 250 PHE CB HB2 sing N N 251 PHE CB HB3 sing N N 252 PHE CG CD1 doub Y N 253 PHE CG CD2 sing Y N 254 PHE CD1 CE1 sing Y N 255 PHE CD1 HD1 sing N N 256 PHE CD2 CE2 doub Y N 257 PHE CD2 HD2 sing N N 258 PHE CE1 CZ doub Y N 259 PHE CE1 HE1 sing N N 260 PHE CE2 CZ sing Y N 261 PHE CE2 HE2 sing N N 262 PHE CZ HZ sing N N 263 PHE OXT HXT sing N N 264 PRO N CA sing N N 265 PRO N CD sing N N 266 PRO N H sing N N 267 PRO CA C sing N N 268 PRO CA CB sing N N 269 PRO CA HA sing N N 270 PRO C O doub N N 271 PRO C OXT sing N N 272 PRO CB CG sing N N 273 PRO CB HB2 sing N N 274 PRO CB HB3 sing N N 275 PRO CG CD sing N N 276 PRO CG HG2 sing N N 277 PRO CG HG3 sing N N 278 PRO CD HD2 sing N N 279 PRO CD HD3 sing N N 280 PRO OXT HXT sing N N 281 SER N CA sing N N 282 SER N H sing N N 283 SER N H2 sing N N 284 SER CA C sing N N 285 SER CA CB sing N N 286 SER CA HA sing N N 287 SER C O doub N N 288 SER C OXT sing N N 289 SER CB OG sing N N 290 SER CB HB2 sing N N 291 SER CB HB3 sing N N 292 SER OG HG sing N N 293 SER OXT HXT sing N N 294 THR N CA sing N N 295 THR N H sing N N 296 THR N H2 sing N N 297 THR CA C sing N N 298 THR CA CB sing N N 299 THR CA HA sing N N 300 THR C O doub N N 301 THR C OXT sing N N 302 THR CB OG1 sing N N 303 THR CB CG2 sing N N 304 THR CB HB sing N N 305 THR OG1 HG1 sing N N 306 THR CG2 HG21 sing N N 307 THR CG2 HG22 sing N N 308 THR CG2 HG23 sing N N 309 THR OXT HXT sing N N 310 TRP N CA sing N N 311 TRP N H sing N N 312 TRP N H2 sing N N 313 TRP CA C sing N N 314 TRP CA CB sing N N 315 TRP CA HA sing N N 316 TRP C O doub N N 317 TRP C OXT sing N N 318 TRP CB CG sing N N 319 TRP CB HB2 sing N N 320 TRP CB HB3 sing N N 321 TRP CG CD1 doub Y N 322 TRP CG CD2 sing Y N 323 TRP CD1 NE1 sing Y N 324 TRP CD1 HD1 sing N N 325 TRP CD2 CE2 doub Y N 326 TRP CD2 CE3 sing Y N 327 TRP NE1 CE2 sing Y N 328 TRP NE1 HE1 sing N N 329 TRP CE2 CZ2 sing Y N 330 TRP CE3 CZ3 doub Y N 331 TRP CE3 HE3 sing N N 332 TRP CZ2 CH2 doub Y N 333 TRP CZ2 HZ2 sing N N 334 TRP CZ3 CH2 sing Y N 335 TRP CZ3 HZ3 sing N N 336 TRP CH2 HH2 sing N N 337 TRP OXT HXT sing N N 338 TYR N CA sing N N 339 TYR N H sing N N 340 TYR N H2 sing N N 341 TYR CA C sing N N 342 TYR CA CB sing N N 343 TYR CA HA sing N N 344 TYR C O doub N N 345 TYR C OXT sing N N 346 TYR CB CG sing N N 347 TYR CB HB2 sing N N 348 TYR CB HB3 sing N N 349 TYR CG CD1 doub Y N 350 TYR CG CD2 sing Y N 351 TYR CD1 CE1 sing Y N 352 TYR CD1 HD1 sing N N 353 TYR CD2 CE2 doub Y N 354 TYR CD2 HD2 sing N N 355 TYR CE1 CZ doub Y N 356 TYR CE1 HE1 sing N N 357 TYR CE2 CZ sing Y N 358 TYR CE2 HE2 sing N N 359 TYR CZ OH sing N N 360 TYR OH HH sing N N 361 TYR OXT HXT sing N N 362 UM3 N1 C2 sing Y N 363 UM3 N1 C6 sing Y N 364 UM3 N1 "C1'" sing N N 365 UM3 C2 N3 sing Y N 366 UM3 C2 O2 doub N N 367 UM3 N3 C4 sing Y N 368 UM3 N3 HN3 sing N N 369 UM3 C4 C5 sing Y N 370 UM3 C4 O4 doub N N 371 UM3 C5 C6 doub Y N 372 UM3 C5 H5 sing N N 373 UM3 C6 H6 sing N N 374 UM3 "C1'" "C2'" sing N N 375 UM3 "C1'" "O4'" sing N N 376 UM3 "C1'" "H1'" sing N N 377 UM3 "C2'" "C3'" sing N N 378 UM3 "C2'" "H2'1" sing N N 379 UM3 "C2'" "H2'2" sing N N 380 UM3 "C3'" "C4'" sing N N 381 UM3 "C3'" "O3'" sing N N 382 UM3 "C3'" "H3'" sing N N 383 UM3 "C4'" "O4'" sing N N 384 UM3 "C4'" "C5'" sing N N 385 UM3 "C4'" "H4'" sing N N 386 UM3 "O3'" P sing N N 387 UM3 "C5'" "O5'" sing N N 388 UM3 "C5'" "H5'1" sing N N 389 UM3 "C5'" "H5'2" sing N N 390 UM3 "O5'" "HO5'" sing N N 391 UM3 P O1P doub N N 392 UM3 P O2P sing N N 393 UM3 P O3P sing N N 394 UM3 O2P HOP2 sing N N 395 UM3 O3P HOP3 sing N N 396 VAL N CA sing N N 397 VAL N H sing N N 398 VAL N H2 sing N N 399 VAL CA C sing N N 400 VAL CA CB sing N N 401 VAL CA HA sing N N 402 VAL C O doub N N 403 VAL C OXT sing N N 404 VAL CB CG1 sing N N 405 VAL CB CG2 sing N N 406 VAL CB HB sing N N 407 VAL CG1 HG11 sing N N 408 VAL CG1 HG12 sing N N 409 VAL CG1 HG13 sing N N 410 VAL CG2 HG21 sing N N 411 VAL CG2 HG22 sing N N 412 VAL CG2 HG23 sing N N 413 VAL OXT HXT sing N N 414 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE' 3PD 3 ;2'-DEOXYURIDINE 3'-MONOPHOSPHATE ; UM3 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2DJH _pdbx_initial_refinement_model.details ? #