data_3B89 # _entry.id 3B89 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.338 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3B89 RCSB RCSB045202 WWPDB D_1000045202 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id NYSGXRC-10094b _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3B89 _pdbx_database_status.recvd_initial_deposition_date 2007-10-31 _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 Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Eswaramoorthy, S.' 1 ? 'Burley, S.K.' 2 0000-0002-2487-9713 'Swaminathan, S.' 3 ? 'New York SGX Research Center for Structural Genomics (NYSGXRC)' 4 ? # _citation.id primary _citation.title 'Crystal structure of rRNA methylase from Escherichia coli.' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Eswaramoorthy, S.' 1 ? primary 'Burley, S.K.' 2 0000-0002-2487-9713 primary 'Swaminathan, S.' 3 ? # _cell.entry_id 3B89 _cell.length_a 56.262 _cell.length_b 94.131 _cell.length_c 96.230 _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 3B89 _symmetry.space_group_name_H-M 'I 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _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 '16S rRNA methylase' 27651.295 1 ? ? ? ? 2 non-polymer syn "GUANOSINE-5'-MONOPHOSPHATE" 363.221 1 ? ? ? ? 3 water nat water 18.015 40 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name '16S ribosomal RNA methylase' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;SLNINDALTSILASKKYRALCPDTVRRILTEEWGRHKSPKQTVEAARTRLHGICGAYVTPESLKAAAAALSAGDVKKALS LHASTKERLAELDTLYDFIFSAETPRRVLDIACGLNPLALYERGIASVWGCDIHQGLGDVITPFAREKDWDFTFALQDVL CAPPAEAGDLALIFKLLPLLEREQAGSA(MSE)ALLQSLNTPR(MSE)AVSFPTRSLGGRGKG(MSE)EANYAAWFEGGL PAEFEIEDKKTIGTELIYLIKKNG ; _entity_poly.pdbx_seq_one_letter_code_can ;SLNINDALTSILASKKYRALCPDTVRRILTEEWGRHKSPKQTVEAARTRLHGICGAYVTPESLKAAAAALSAGDVKKALS LHASTKERLAELDTLYDFIFSAETPRRVLDIACGLNPLALYERGIASVWGCDIHQGLGDVITPFAREKDWDFTFALQDVL CAPPAEAGDLALIFKLLPLLEREQAGSAMALLQSLNTPRMAVSFPTRSLGGRGKGMEANYAAWFEGGLPAEFEIEDKKTI GTELIYLIKKNG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier NYSGXRC-10094b # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 LEU n 1 3 ASN n 1 4 ILE n 1 5 ASN n 1 6 ASP n 1 7 ALA n 1 8 LEU n 1 9 THR n 1 10 SER n 1 11 ILE n 1 12 LEU n 1 13 ALA n 1 14 SER n 1 15 LYS n 1 16 LYS n 1 17 TYR n 1 18 ARG n 1 19 ALA n 1 20 LEU n 1 21 CYS n 1 22 PRO n 1 23 ASP n 1 24 THR n 1 25 VAL n 1 26 ARG n 1 27 ARG n 1 28 ILE n 1 29 LEU n 1 30 THR n 1 31 GLU n 1 32 GLU n 1 33 TRP n 1 34 GLY n 1 35 ARG n 1 36 HIS n 1 37 LYS n 1 38 SER n 1 39 PRO n 1 40 LYS n 1 41 GLN n 1 42 THR n 1 43 VAL n 1 44 GLU n 1 45 ALA n 1 46 ALA n 1 47 ARG n 1 48 THR n 1 49 ARG n 1 50 LEU n 1 51 HIS n 1 52 GLY n 1 53 ILE n 1 54 CYS n 1 55 GLY n 1 56 ALA n 1 57 TYR n 1 58 VAL n 1 59 THR n 1 60 PRO n 1 61 GLU n 1 62 SER n 1 63 LEU n 1 64 LYS n 1 65 ALA n 1 66 ALA n 1 67 ALA n 1 68 ALA n 1 69 ALA n 1 70 LEU n 1 71 SER n 1 72 ALA n 1 73 GLY n 1 74 ASP n 1 75 VAL n 1 76 LYS n 1 77 LYS n 1 78 ALA n 1 79 LEU n 1 80 SER n 1 81 LEU n 1 82 HIS n 1 83 ALA n 1 84 SER n 1 85 THR n 1 86 LYS n 1 87 GLU n 1 88 ARG n 1 89 LEU n 1 90 ALA n 1 91 GLU n 1 92 LEU n 1 93 ASP n 1 94 THR n 1 95 LEU n 1 96 TYR n 1 97 ASP n 1 98 PHE n 1 99 ILE n 1 100 PHE n 1 101 SER n 1 102 ALA n 1 103 GLU n 1 104 THR n 1 105 PRO n 1 106 ARG n 1 107 ARG n 1 108 VAL n 1 109 LEU n 1 110 ASP n 1 111 ILE n 1 112 ALA n 1 113 CYS n 1 114 GLY n 1 115 LEU n 1 116 ASN n 1 117 PRO n 1 118 LEU n 1 119 ALA n 1 120 LEU n 1 121 TYR n 1 122 GLU n 1 123 ARG n 1 124 GLY n 1 125 ILE n 1 126 ALA n 1 127 SER n 1 128 VAL n 1 129 TRP n 1 130 GLY n 1 131 CYS n 1 132 ASP n 1 133 ILE n 1 134 HIS n 1 135 GLN n 1 136 GLY n 1 137 LEU n 1 138 GLY n 1 139 ASP n 1 140 VAL n 1 141 ILE n 1 142 THR n 1 143 PRO n 1 144 PHE n 1 145 ALA n 1 146 ARG n 1 147 GLU n 1 148 LYS n 1 149 ASP n 1 150 TRP n 1 151 ASP n 1 152 PHE n 1 153 THR n 1 154 PHE n 1 155 ALA n 1 156 LEU n 1 157 GLN n 1 158 ASP n 1 159 VAL n 1 160 LEU n 1 161 CYS n 1 162 ALA n 1 163 PRO n 1 164 PRO n 1 165 ALA n 1 166 GLU n 1 167 ALA n 1 168 GLY n 1 169 ASP n 1 170 LEU n 1 171 ALA n 1 172 LEU n 1 173 ILE n 1 174 PHE n 1 175 LYS n 1 176 LEU n 1 177 LEU n 1 178 PRO n 1 179 LEU n 1 180 LEU n 1 181 GLU n 1 182 ARG n 1 183 GLU n 1 184 GLN n 1 185 ALA n 1 186 GLY n 1 187 SER n 1 188 ALA n 1 189 MSE n 1 190 ALA n 1 191 LEU n 1 192 LEU n 1 193 GLN n 1 194 SER n 1 195 LEU n 1 196 ASN n 1 197 THR n 1 198 PRO n 1 199 ARG n 1 200 MSE n 1 201 ALA n 1 202 VAL n 1 203 SER n 1 204 PHE n 1 205 PRO n 1 206 THR n 1 207 ARG n 1 208 SER n 1 209 LEU n 1 210 GLY n 1 211 GLY n 1 212 ARG n 1 213 GLY n 1 214 LYS n 1 215 GLY n 1 216 MSE n 1 217 GLU n 1 218 ALA n 1 219 ASN n 1 220 TYR n 1 221 ALA n 1 222 ALA n 1 223 TRP n 1 224 PHE n 1 225 GLU n 1 226 GLY n 1 227 GLY n 1 228 LEU n 1 229 PRO n 1 230 ALA n 1 231 GLU n 1 232 PHE n 1 233 GLU n 1 234 ILE n 1 235 GLU n 1 236 ASP n 1 237 LYS n 1 238 LYS n 1 239 THR n 1 240 ILE n 1 241 GLY n 1 242 THR n 1 243 GLU n 1 244 LEU n 1 245 ILE n 1 246 TYR n 1 247 LEU n 1 248 ILE n 1 249 LYS n 1 250 LYS n 1 251 ASN n 1 252 GLY n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus Escherichia _entity_src_gen.pdbx_gene_src_gene rmtB _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 Escherichia _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 Q763K9_ECOLX _struct_ref.pdbx_db_accession Q763K9 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;NINDALTSILASKKYRALCPDTVRRILTEEWGRHKSPKQTVEAARTRLHGICGAYVTPESLKAAAAALSAGDVKKALSLH ASTKERLAELDTLYDFIFSAETPRRVLDIACGLNPLALYERGIASVWGCDIHQGLGDVITPFAREKDWDFTFALQDVLCA PPAEAGDLALIFKLLPLLEREQAGSAMALLQSLNTPRMAVSFPTRSLGGRGKGMEANYAAWFEGGLPAEFEIEDKKTIGT ELIYLIKKNG ; _struct_ref.pdbx_align_begin 2 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3B89 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 252 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q763K9 _struct_ref_seq.db_align_beg 2 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 251 _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 251 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3B89 SER A 1 ? UNP Q763K9 ? ? 'expression tag' 0 1 1 3B89 LEU A 2 ? UNP Q763K9 ? ? 'expression tag' 1 2 # 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 5GP non-polymer . "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 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 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3B89 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.30 _exptl_crystal.density_percent_sol 46.61 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '0.1M Bis-Tris, 28% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2007-06-28 _diffrn_detector.details Mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X29A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X29A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 3B89 _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 2.6 _reflns.d_resolution_low 50.0 _reflns.number_all 7962 _reflns.number_obs 7962 _reflns.percent_possible_obs 97.8 _reflns.pdbx_Rmerge_I_obs 0.077 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 11.4 _reflns.B_iso_Wilson_estimate 18.1 _reflns.pdbx_redundancy 12.1 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.6 _reflns_shell.d_res_low 2.69 _reflns_shell.percent_possible_all 83.8 _reflns_shell.Rmerge_I_obs 0.282 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 5.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 673 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3B89 _refine.ls_d_res_high 2.6 _refine.ls_d_res_low 50.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I 0.0 _refine.ls_number_reflns_all 7746 _refine.ls_number_reflns_obs 7746 _refine.ls_number_reflns_R_free 745 _refine.ls_percent_reflns_obs 94.9 _refine.ls_R_factor_all 0.266 _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.2265 _refine.ls_R_factor_R_free 0.2824 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean 35.1 _refine.aniso_B[1][1] -8.55 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][2] 3.01 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] 5.54 _refine.details ;Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines. ; _refine.B_iso_min ? _refine.B_iso_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3B89 _refine_analyze.Luzzati_coordinate_error_obs 0.34 _refine_analyze.Luzzati_sigma_a_obs 0.41 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.43 _refine_analyze.Luzzati_sigma_a_free 0.41 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1843 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 24 _refine_hist.number_atoms_solvent 40 _refine_hist.number_atoms_total 1907 _refine_hist.d_res_high 2.6 _refine_hist.d_res_low 50.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.5 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_deg 22.8 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_deg 0.94 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.6 _refine_ls_shell.d_res_low 2.76 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.316 _refine_ls_shell.percent_reflns_obs 78.4 _refine_ls_shell.R_factor_R_free 0.328 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 94 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 934 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3B89 _struct.title 'Crystal structure of rRNA methylase from Escherichia coli' _struct.pdbx_descriptor '16S rRNA methylase' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3B89 _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text ;10094b, NYSGXRC, rmtB, Structural Genomics, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, Methyltransferase, Plasmid, TRANSFERASE ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASN A 3 ? LEU A 12 ? ASN A 2 LEU A 11 1 ? 10 HELX_P HELX_P2 2 CYS A 21 ? ARG A 35 ? CYS A 20 ARG A 34 1 ? 15 HELX_P HELX_P3 3 THR A 42 ? GLY A 52 ? THR A 41 GLY A 51 1 ? 11 HELX_P HELX_P4 4 THR A 59 ? ALA A 72 ? THR A 58 ALA A 71 1 ? 14 HELX_P HELX_P5 5 ASP A 74 ? LEU A 81 ? ASP A 73 LEU A 80 1 ? 8 HELX_P HELX_P6 6 HIS A 82 ? ARG A 88 ? HIS A 81 ARG A 87 1 ? 7 HELX_P HELX_P7 7 GLU A 91 ? SER A 101 ? GLU A 90 SER A 100 1 ? 11 HELX_P HELX_P8 8 ASN A 116 ? GLU A 122 ? ASN A 115 GLU A 121 1 ? 7 HELX_P HELX_P9 9 HIS A 134 ? GLU A 147 ? HIS A 133 GLU A 146 1 ? 14 HELX_P HELX_P10 10 LEU A 176 ? GLN A 184 ? LEU A 175 GLN A 183 1 ? 9 HELX_P HELX_P11 11 GLY A 186 ? SER A 194 ? GLY A 185 SER A 193 1 ? 9 HELX_P HELX_P12 12 ASN A 219 ? LEU A 228 ? ASN A 218 LEU A 227 1 ? 10 # _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 _struct_conn.pdbx_role covale1 covale both ? A ALA 188 C ? ? ? 1_555 A MSE 189 N ? ? A ALA 187 A MSE 188 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale2 covale both ? A MSE 189 C ? ? ? 1_555 A ALA 190 N ? ? A MSE 188 A ALA 189 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale3 covale both ? A ARG 199 C ? ? ? 1_555 A MSE 200 N ? ? A ARG 198 A MSE 199 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale4 covale both ? A MSE 200 C ? ? ? 1_555 A ALA 201 N ? ? A MSE 199 A ALA 200 1_555 ? ? ? ? ? ? ? 1.325 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 7 _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 ? parallel A 2 3 ? parallel A 3 4 ? parallel A 4 5 ? parallel A 5 6 ? anti-parallel A 6 7 ? 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 ASP A 151 ? LEU A 156 ? ASP A 150 LEU A 155 A 2 SER A 127 ? ASP A 132 ? SER A 126 ASP A 131 A 3 ARG A 107 ? ILE A 111 ? ARG A 106 ILE A 110 A 4 LEU A 170 ? ILE A 173 ? LEU A 169 ILE A 172 A 5 ARG A 199 ? PRO A 205 ? ARG A 198 PRO A 204 A 6 GLU A 243 ? LYS A 250 ? GLU A 242 LYS A 249 A 7 PHE A 232 ? ILE A 240 ? PHE A 231 ILE A 239 # 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 153 ? O THR A 152 N GLY A 130 ? N GLY A 129 A 2 3 O TRP A 129 ? O TRP A 128 N VAL A 108 ? N VAL A 107 A 3 4 N LEU A 109 ? N LEU A 108 O LEU A 170 ? O LEU A 169 A 4 5 N ILE A 173 ? N ILE A 172 O ALA A 201 ? O ALA A 200 A 5 6 N VAL A 202 ? N VAL A 201 O TYR A 246 ? O TYR A 245 A 6 7 O ILE A 245 ? O ILE A 244 N LYS A 238 ? N LYS A 237 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id 5GP _struct_site.pdbx_auth_seq_id 500 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 12 _struct_site.details 'BINDING SITE FOR RESIDUE 5GP A 500' # 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 12 CYS A 54 ? CYS A 53 . ? 1_555 ? 2 AC1 12 HIS A 82 ? HIS A 81 . ? 1_555 ? 3 AC1 12 SER A 84 ? SER A 83 . ? 1_555 ? 4 AC1 12 ALA A 112 ? ALA A 111 . ? 1_555 ? 5 AC1 12 ASP A 132 ? ASP A 131 . ? 1_555 ? 6 AC1 12 ILE A 133 ? ILE A 132 . ? 1_555 ? 7 AC1 12 GLN A 157 ? GLN A 156 . ? 1_555 ? 8 AC1 12 ASP A 158 ? ASP A 157 . ? 1_555 ? 9 AC1 12 VAL A 159 ? VAL A 158 . ? 1_555 ? 10 AC1 12 PHE A 174 ? PHE A 173 . ? 1_555 ? 11 AC1 12 LYS A 175 ? LYS A 174 . ? 1_555 ? 12 AC1 12 HOH C . ? HOH A 522 . ? 1_555 ? # _database_PDB_matrix.entry_id 3B89 _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 3B89 _atom_sites.fract_transf_matrix[1][1] 0.017774 _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] 0.010623 _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] 0.010392 _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 SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 SER 1 0 ? ? ? A . n A 1 2 LEU 2 1 ? ? ? A . n A 1 3 ASN 3 2 2 ASN ASN A . n A 1 4 ILE 4 3 3 ILE ILE A . n A 1 5 ASN 5 4 4 ASN ASN A . n A 1 6 ASP 6 5 5 ASP ASP A . n A 1 7 ALA 7 6 6 ALA ALA A . n A 1 8 LEU 8 7 7 LEU LEU A . n A 1 9 THR 9 8 8 THR THR A . n A 1 10 SER 10 9 9 SER SER A . n A 1 11 ILE 11 10 10 ILE ILE A . n A 1 12 LEU 12 11 11 LEU LEU A . n A 1 13 ALA 13 12 12 ALA ALA A . n A 1 14 SER 14 13 13 SER SER A . n A 1 15 LYS 15 14 14 LYS LYS A . n A 1 16 LYS 16 15 15 LYS LYS A . n A 1 17 TYR 17 16 16 TYR TYR A . n A 1 18 ARG 18 17 17 ARG ARG A . n A 1 19 ALA 19 18 18 ALA ALA A . n A 1 20 LEU 20 19 19 LEU LEU A . n A 1 21 CYS 21 20 20 CYS CYS A . n A 1 22 PRO 22 21 21 PRO PRO A . n A 1 23 ASP 23 22 22 ASP ASP A . n A 1 24 THR 24 23 23 THR THR A . n A 1 25 VAL 25 24 24 VAL VAL A . n A 1 26 ARG 26 25 25 ARG ARG A . n A 1 27 ARG 27 26 26 ARG ARG A . n A 1 28 ILE 28 27 27 ILE ILE A . n A 1 29 LEU 29 28 28 LEU LEU A . n A 1 30 THR 30 29 29 THR THR A . n A 1 31 GLU 31 30 30 GLU GLU A . n A 1 32 GLU 32 31 31 GLU GLU A . n A 1 33 TRP 33 32 32 TRP TRP A . n A 1 34 GLY 34 33 33 GLY GLY A . n A 1 35 ARG 35 34 34 ARG ARG A . n A 1 36 HIS 36 35 35 HIS HIS A . n A 1 37 LYS 37 36 36 LYS LYS A . n A 1 38 SER 38 37 37 SER SER A . n A 1 39 PRO 39 38 38 PRO PRO A . n A 1 40 LYS 40 39 39 LYS LYS A . n A 1 41 GLN 41 40 40 GLN GLN A . n A 1 42 THR 42 41 41 THR THR A . n A 1 43 VAL 43 42 42 VAL VAL A . n A 1 44 GLU 44 43 43 GLU GLU A . n A 1 45 ALA 45 44 44 ALA ALA A . n A 1 46 ALA 46 45 45 ALA ALA A . n A 1 47 ARG 47 46 46 ARG ARG A . n A 1 48 THR 48 47 47 THR THR A . n A 1 49 ARG 49 48 48 ARG ARG A . n A 1 50 LEU 50 49 49 LEU LEU A . n A 1 51 HIS 51 50 50 HIS HIS A . n A 1 52 GLY 52 51 51 GLY GLY A . n A 1 53 ILE 53 52 52 ILE ILE A . n A 1 54 CYS 54 53 53 CYS CYS A . n A 1 55 GLY 55 54 54 GLY GLY A . n A 1 56 ALA 56 55 55 ALA ALA A . n A 1 57 TYR 57 56 ? ? ? A . n A 1 58 VAL 58 57 57 VAL ALA A . n A 1 59 THR 59 58 58 THR THR A . n A 1 60 PRO 60 59 59 PRO PRO A . n A 1 61 GLU 61 60 60 GLU GLU A . n A 1 62 SER 62 61 61 SER SER A . n A 1 63 LEU 63 62 62 LEU LEU A . n A 1 64 LYS 64 63 63 LYS LYS A . n A 1 65 ALA 65 64 64 ALA ALA A . n A 1 66 ALA 66 65 65 ALA ALA A . n A 1 67 ALA 67 66 66 ALA ALA A . n A 1 68 ALA 68 67 67 ALA ALA A . n A 1 69 ALA 69 68 68 ALA ALA A . n A 1 70 LEU 70 69 69 LEU LEU A . n A 1 71 SER 71 70 70 SER SER A . n A 1 72 ALA 72 71 71 ALA ALA A . n A 1 73 GLY 73 72 72 GLY GLY A . n A 1 74 ASP 74 73 73 ASP ASP A . n A 1 75 VAL 75 74 74 VAL VAL A . n A 1 76 LYS 76 75 75 LYS LYS A . n A 1 77 LYS 77 76 76 LYS LYS A . n A 1 78 ALA 78 77 77 ALA ALA A . n A 1 79 LEU 79 78 78 LEU LEU A . n A 1 80 SER 80 79 79 SER SER A . n A 1 81 LEU 81 80 80 LEU LEU A . n A 1 82 HIS 82 81 81 HIS HIS A . n A 1 83 ALA 83 82 82 ALA ALA A . n A 1 84 SER 84 83 83 SER SER A . n A 1 85 THR 85 84 84 THR THR A . n A 1 86 LYS 86 85 85 LYS LYS A . n A 1 87 GLU 87 86 86 GLU GLU A . n A 1 88 ARG 88 87 87 ARG ARG A . n A 1 89 LEU 89 88 88 LEU LEU A . n A 1 90 ALA 90 89 89 ALA ALA A . n A 1 91 GLU 91 90 90 GLU GLU A . n A 1 92 LEU 92 91 91 LEU LEU A . n A 1 93 ASP 93 92 92 ASP ASP A . n A 1 94 THR 94 93 93 THR THR A . n A 1 95 LEU 95 94 94 LEU LEU A . n A 1 96 TYR 96 95 95 TYR TYR A . n A 1 97 ASP 97 96 96 ASP ASP A . n A 1 98 PHE 98 97 97 PHE PHE A . n A 1 99 ILE 99 98 98 ILE ILE A . n A 1 100 PHE 100 99 99 PHE PHE A . n A 1 101 SER 101 100 100 SER SER A . n A 1 102 ALA 102 101 101 ALA ALA A . n A 1 103 GLU 103 102 102 GLU GLU A . n A 1 104 THR 104 103 103 THR THR A . n A 1 105 PRO 105 104 104 PRO PRO A . n A 1 106 ARG 106 105 105 ARG ARG A . n A 1 107 ARG 107 106 106 ARG ARG A . n A 1 108 VAL 108 107 107 VAL VAL A . n A 1 109 LEU 109 108 108 LEU LEU A . n A 1 110 ASP 110 109 109 ASP ASP A . n A 1 111 ILE 111 110 110 ILE ILE A . n A 1 112 ALA 112 111 111 ALA ALA A . n A 1 113 CYS 113 112 112 CYS CYS A . n A 1 114 GLY 114 113 113 GLY GLY A . n A 1 115 LEU 115 114 114 LEU LEU A . n A 1 116 ASN 116 115 115 ASN ASN A . n A 1 117 PRO 117 116 116 PRO PRO A . n A 1 118 LEU 118 117 117 LEU LEU A . n A 1 119 ALA 119 118 118 ALA ALA A . n A 1 120 LEU 120 119 119 LEU LEU A . n A 1 121 TYR 121 120 120 TYR TYR A . n A 1 122 GLU 122 121 121 GLU GLU A . n A 1 123 ARG 123 122 122 ARG ARG A . n A 1 124 GLY 124 123 123 GLY GLY A . n A 1 125 ILE 125 124 124 ILE ILE A . n A 1 126 ALA 126 125 125 ALA ALA A . n A 1 127 SER 127 126 126 SER SER A . n A 1 128 VAL 128 127 127 VAL VAL A . n A 1 129 TRP 129 128 128 TRP TRP A . n A 1 130 GLY 130 129 129 GLY GLY A . n A 1 131 CYS 131 130 130 CYS CYS A . n A 1 132 ASP 132 131 131 ASP ASP A . n A 1 133 ILE 133 132 132 ILE ILE A . n A 1 134 HIS 134 133 133 HIS HIS A . n A 1 135 GLN 135 134 134 GLN GLN A . n A 1 136 GLY 136 135 135 GLY GLY A . n A 1 137 LEU 137 136 136 LEU LEU A . n A 1 138 GLY 138 137 137 GLY GLY A . n A 1 139 ASP 139 138 138 ASP ASP A . n A 1 140 VAL 140 139 139 VAL VAL A . n A 1 141 ILE 141 140 140 ILE ILE A . n A 1 142 THR 142 141 141 THR THR A . n A 1 143 PRO 143 142 142 PRO PRO A . n A 1 144 PHE 144 143 143 PHE PHE A . n A 1 145 ALA 145 144 144 ALA ALA A . n A 1 146 ARG 146 145 145 ARG ALA A . n A 1 147 GLU 147 146 146 GLU GLU A . n A 1 148 LYS 148 147 147 LYS LYS A . n A 1 149 ASP 149 148 148 ASP ASP A . n A 1 150 TRP 150 149 149 TRP TRP A . n A 1 151 ASP 151 150 150 ASP ASP A . n A 1 152 PHE 152 151 151 PHE PHE A . n A 1 153 THR 153 152 152 THR THR A . n A 1 154 PHE 154 153 153 PHE PHE A . n A 1 155 ALA 155 154 154 ALA ALA A . n A 1 156 LEU 156 155 155 LEU LEU A . n A 1 157 GLN 157 156 156 GLN GLN A . n A 1 158 ASP 158 157 157 ASP ASP A . n A 1 159 VAL 159 158 158 VAL VAL A . n A 1 160 LEU 160 159 159 LEU LEU A . n A 1 161 CYS 161 160 160 CYS CYS A . n A 1 162 ALA 162 161 161 ALA ALA A . n A 1 163 PRO 163 162 162 PRO PRO A . n A 1 164 PRO 164 163 163 PRO PRO A . n A 1 165 ALA 165 164 164 ALA ALA A . n A 1 166 GLU 166 165 165 GLU GLU A . n A 1 167 ALA 167 166 166 ALA ALA A . n A 1 168 GLY 168 167 167 GLY GLY A . n A 1 169 ASP 169 168 168 ASP ASP A . n A 1 170 LEU 170 169 169 LEU LEU A . n A 1 171 ALA 171 170 170 ALA ALA A . n A 1 172 LEU 172 171 171 LEU LEU A . n A 1 173 ILE 173 172 172 ILE ILE A . n A 1 174 PHE 174 173 173 PHE PHE A . n A 1 175 LYS 175 174 174 LYS LYS A . n A 1 176 LEU 176 175 175 LEU LEU A . n A 1 177 LEU 177 176 176 LEU LEU A . n A 1 178 PRO 178 177 177 PRO PRO A . n A 1 179 LEU 179 178 178 LEU LEU A . n A 1 180 LEU 180 179 179 LEU LEU A . n A 1 181 GLU 181 180 180 GLU GLU A . n A 1 182 ARG 182 181 181 ARG ARG A . n A 1 183 GLU 183 182 182 GLU GLU A . n A 1 184 GLN 184 183 183 GLN GLN A . n A 1 185 ALA 185 184 184 ALA ALA A . n A 1 186 GLY 186 185 185 GLY GLY A . n A 1 187 SER 187 186 186 SER SER A . n A 1 188 ALA 188 187 187 ALA ALA A . n A 1 189 MSE 189 188 188 MSE MSE A . n A 1 190 ALA 190 189 189 ALA ALA A . n A 1 191 LEU 191 190 190 LEU LEU A . n A 1 192 LEU 192 191 191 LEU LEU A . n A 1 193 GLN 193 192 192 GLN GLN A . n A 1 194 SER 194 193 193 SER SER A . n A 1 195 LEU 195 194 194 LEU LEU A . n A 1 196 ASN 196 195 195 ASN ASN A . n A 1 197 THR 197 196 196 THR THR A . n A 1 198 PRO 198 197 197 PRO PRO A . n A 1 199 ARG 199 198 198 ARG ARG A . n A 1 200 MSE 200 199 199 MSE MSE A . n A 1 201 ALA 201 200 200 ALA ALA A . n A 1 202 VAL 202 201 201 VAL VAL A . n A 1 203 SER 203 202 202 SER SER A . n A 1 204 PHE 204 203 203 PHE PHE A . n A 1 205 PRO 205 204 204 PRO PRO A . n A 1 206 THR 206 205 205 THR THR A . n A 1 207 ARG 207 206 206 ARG ARG A . n A 1 208 SER 208 207 207 SER SER A . n A 1 209 LEU 209 208 ? ? ? A . n A 1 210 GLY 210 209 ? ? ? A . n A 1 211 GLY 211 210 ? ? ? A . n A 1 212 ARG 212 211 ? ? ? A . n A 1 213 GLY 213 212 ? ? ? A . n A 1 214 LYS 214 213 ? ? ? A . n A 1 215 GLY 215 214 ? ? ? A . n A 1 216 MSE 216 215 ? ? ? A . n A 1 217 GLU 217 216 216 GLU GLU A . n A 1 218 ALA 218 217 217 ALA ALA A . n A 1 219 ASN 219 218 218 ASN ASN A . n A 1 220 TYR 220 219 219 TYR TYR A . n A 1 221 ALA 221 220 220 ALA ALA A . n A 1 222 ALA 222 221 221 ALA ALA A . n A 1 223 TRP 223 222 222 TRP TRP A . n A 1 224 PHE 224 223 223 PHE PHE A . n A 1 225 GLU 225 224 224 GLU GLU A . n A 1 226 GLY 226 225 225 GLY GLY A . n A 1 227 GLY 227 226 226 GLY GLY A . n A 1 228 LEU 228 227 227 LEU LEU A . n A 1 229 PRO 229 228 228 PRO PRO A . n A 1 230 ALA 230 229 229 ALA ALA A . n A 1 231 GLU 231 230 230 GLU GLU A . n A 1 232 PHE 232 231 231 PHE PHE A . n A 1 233 GLU 233 232 232 GLU GLU A . n A 1 234 ILE 234 233 233 ILE ILE A . n A 1 235 GLU 235 234 234 GLU GLU A . n A 1 236 ASP 236 235 235 ASP ASP A . n A 1 237 LYS 237 236 236 LYS LYS A . n A 1 238 LYS 238 237 237 LYS LYS A . n A 1 239 THR 239 238 238 THR THR A . n A 1 240 ILE 240 239 239 ILE ILE A . n A 1 241 GLY 241 240 240 GLY GLY A . n A 1 242 THR 242 241 241 THR THR A . n A 1 243 GLU 243 242 242 GLU GLU A . n A 1 244 LEU 244 243 243 LEU LEU A . n A 1 245 ILE 245 244 244 ILE ILE A . n A 1 246 TYR 246 245 245 TYR TYR A . n A 1 247 LEU 247 246 246 LEU LEU A . n A 1 248 ILE 248 247 247 ILE ILE A . n A 1 249 LYS 249 248 248 LYS LYS A . n A 1 250 LYS 250 249 249 LYS LYS A . n A 1 251 ASN 251 250 250 ASN ASN A . n A 1 252 GLY 252 251 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'New York SGX Research Center for Structural Genomics' _pdbx_SG_project.initial_of_center NYSGXRC # 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 5GP 1 500 500 5GP 5GP A . C 3 HOH 1 501 1 HOH TIP A . C 3 HOH 2 502 2 HOH TIP A . C 3 HOH 3 503 4 HOH TIP A . C 3 HOH 4 504 5 HOH TIP A . C 3 HOH 5 505 6 HOH TIP A . C 3 HOH 6 506 7 HOH TIP A . C 3 HOH 7 507 8 HOH TIP A . C 3 HOH 8 508 9 HOH TIP A . C 3 HOH 9 509 10 HOH TIP A . C 3 HOH 10 510 11 HOH TIP A . C 3 HOH 11 511 12 HOH TIP A . C 3 HOH 12 512 13 HOH TIP A . C 3 HOH 13 513 14 HOH TIP A . C 3 HOH 14 514 15 HOH TIP A . C 3 HOH 15 515 16 HOH TIP A . C 3 HOH 16 516 17 HOH TIP A . C 3 HOH 17 517 18 HOH TIP A . C 3 HOH 18 518 19 HOH TIP A . C 3 HOH 19 519 20 HOH TIP A . C 3 HOH 20 520 21 HOH TIP A . C 3 HOH 21 521 22 HOH TIP A . C 3 HOH 22 522 23 HOH TIP A . C 3 HOH 23 523 24 HOH TIP A . C 3 HOH 24 524 25 HOH TIP A . C 3 HOH 25 525 26 HOH TIP A . C 3 HOH 26 526 27 HOH TIP A . C 3 HOH 27 527 28 HOH TIP A . C 3 HOH 28 528 29 HOH TIP A . C 3 HOH 29 529 30 HOH TIP A . C 3 HOH 30 530 31 HOH TIP A . C 3 HOH 31 531 32 HOH TIP A . C 3 HOH 32 532 33 HOH TIP A . C 3 HOH 33 533 34 HOH TIP A . C 3 HOH 34 534 35 HOH TIP A . C 3 HOH 35 535 36 HOH TIP A . C 3 HOH 36 536 37 HOH TIP A . C 3 HOH 37 537 38 HOH TIP A . C 3 HOH 38 538 39 HOH TIP A . C 3 HOH 39 539 40 HOH TIP A . C 3 HOH 40 540 41 HOH TIP A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 189 A MSE 188 ? MET SELENOMETHIONINE 2 A MSE 200 A MSE 199 ? MET SELENOMETHIONINE # _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 # _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 2007-11-27 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2021-02-03 # _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' 'Version format compliance' 2 3 'Structure model' 'Database references' 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' 'Structure summary' # 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' audit_author 2 3 'Structure model' citation_author 3 3 'Structure model' struct_conn 4 3 'Structure model' struct_ref_seq_dif 5 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' '_audit_author.identifier_ORCID' 2 3 'Structure model' '_citation_author.identifier_ORCID' 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 CBASS 'data collection' . ? 1 SOLVE phasing . ? 2 SHARP phasing . ? 3 CNS refinement 1.1 ? 4 HKL-2000 'data reduction' . ? 5 HKL-2000 'data scaling' . ? 6 # 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 HIS A 35 ? ? -136.34 -58.67 2 1 LYS A 36 ? ? 84.09 -13.83 3 1 SER A 37 ? ? 40.10 170.39 4 1 LYS A 39 ? ? 111.64 -42.89 5 1 GLU A 121 ? ? -61.78 4.49 6 1 GLU A 146 ? ? -59.94 -5.71 7 1 LYS A 174 ? ? 29.06 68.44 8 1 LEU A 175 ? ? -140.02 -42.86 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A VAL 57 ? CG1 ? A VAL 58 CG1 2 1 Y 1 A VAL 57 ? CG2 ? A VAL 58 CG2 3 1 Y 1 A ARG 145 ? CG ? A ARG 146 CG 4 1 Y 1 A ARG 145 ? CD ? A ARG 146 CD 5 1 Y 1 A ARG 145 ? NE ? A ARG 146 NE 6 1 Y 1 A ARG 145 ? CZ ? A ARG 146 CZ 7 1 Y 1 A ARG 145 ? NH1 ? A ARG 146 NH1 8 1 Y 1 A ARG 145 ? NH2 ? A ARG 146 NH2 # 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 SER 0 ? A SER 1 2 1 Y 1 A LEU 1 ? A LEU 2 3 1 Y 1 A TYR 56 ? A TYR 57 4 1 Y 1 A LEU 208 ? A LEU 209 5 1 Y 1 A GLY 209 ? A GLY 210 6 1 Y 1 A GLY 210 ? A GLY 211 7 1 Y 1 A ARG 211 ? A ARG 212 8 1 Y 1 A GLY 212 ? A GLY 213 9 1 Y 1 A LYS 213 ? A LYS 214 10 1 Y 1 A GLY 214 ? A GLY 215 11 1 Y 1 A MSE 215 ? A MSE 216 12 1 Y 1 A GLY 251 ? A GLY 252 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "GUANOSINE-5'-MONOPHOSPHATE" 5GP 3 water HOH #